pemsley / coot Goto Github PK

Software for macromolecular model-building

Home Page: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

License: GNU General Public License v3.0

C++ 80.78% Awk 0.05% Shell 2.60% Scheme 3.72% Makefile 0.55% C 2.88% HTML 0.12% Perl 0.27% Python 7.18% NSIS 0.12% Batchfile 0.04% M4 0.75% Roff 0.16% R 0.04% Ruby 0.01% SWIG 0.02% Hack 0.01% CMake 0.10% GLSL 0.60% TeX 0.01%

coot's People

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Watchers

Forkers

bernhardcl jlec benmwebb mjamroz dylanlukes smart111 alexmyczko aj26git jun-lizst keitaroyam andretomasgraca ppichling1 cv-gphl minghao2016 aspirincode erwinp athemis farzaneh-sharif qitsweauca nerilex madcatx blake-riley jcbollinger lusirnoman william3johnson hgonomeg gaorongchao filomenosanchez martinemnoble1 rnaimehaom phymucs stuartjamesmcnicholas ambapant protection4 bkpoon lucreziacatapano stachowskitim rootelmo mysecondnameisdanger odcambc dsclassen

coot's Issues

The script build-it cannot download libccp4-6.5.1.tar.gz from ftp.ccp4.ac.uk

In the script build-it, there is a wget command downloading libccp4-6.5.1.tar.gz from ftp.ccp4.ac.uk.

${WGET} ftp://ftp.ccp4.ac.uk/opensource/libccp4-$libccp4_version.tar.gz

The site ftp.ccp4.ac.uk has been inaccessible for many days. The download eventually fails after 20 failed attempts.

wget ftp://ftp.ccp4.ac.uk/opensource/libccp4-6.5.1.tar.gz
--2022-03-28 11:20:52-- ftp://ftp.ccp4.ac.uk/opensource/libccp4-6.5.1.tar.gz
=> ‘libccp4-6.5.1.tar.gz’
Resolving ftp.ccp4.ac.uk (ftp.ccp4.ac.uk)... 148.79.162.88
Connecting to ftp.ccp4.ac.uk (ftp.ccp4.ac.uk)|148.79.162.88|:21... failed: Connection timed out.
Retrying.

--2022-03-28 11:23:04-- ftp://ftp.ccp4.ac.uk/opensource/libccp4-6.5.1.tar.gz
(try: 2) => ‘libccp4-6.5.1.tar.gz’
Connecting to ftp.ccp4.ac.uk (ftp.ccp4.ac.uk)|148.79.162.88|:21...

Can somebody please take a look?

Thank you!

issue with the gtk3 branch configure code

As of this 10 am CST 4/7/22, I'm seeing this issue from the configuration file on the latest gtk3 branch (I'm running on Rocky Linux 8.5/RHEL 8.5 clone):
$ ./configure
.
.
.

checking if this is MINGW on Windows... no
checking for LIBPNG... yes
checking for CAIRO... yes
checking for SQLite3... no
checking for mmdb2... yes
checking for ssm... yes
no
checking for non-prefixed single-precision FFTW2 (fftw.h)... yes
checking for Clipper... yes
Not using guile
./configure: line 19434: syntax error near unexpected token 1.3,COOT_GSL_FLAGS=-DHAVE_GSL,COOT_GSL_FLAGS=""' ./configure: line 19434: AX_PATH_GSL(1.3,COOT_GSL_FLAGS=-DHAVE_GSL,COOT_GSL_FLAGS="")'

Update backward-cpp library (for M1 Macs)

Hi Paul,

Yoshitaka's Homebrew script is fantastic. Coot pre-1.0 almost builds on the fancy, new M1 processors.

At the moment, compilation on Apple Silicon fails on utils/backward.hpp. A short patch (see bombela/backward-cpp#201) is all that's blocking compilation.

diff --git a/utils/backward.hpp b/utils/backward.hpp
index 195ca8f2d..e661ce7b6 100644
--- a/utils/backward.hpp
+++ b/utils/backward.hpp
@@ -4157,7 +4157,11 @@ class SignalHandling {
 #elif defined(__arm__)
     error_addr = reinterpret_cast<void *>(uctx->uc_mcontext.arm_pc);
 #elif defined(__aarch64__)
-    error_addr = reinterpret_cast<void *>(uctx->uc_mcontext.pc);
+    #if defined(__APPLE__)
+      error_addr = reinterpret_cast<void *>(uctx->uc_mcontext->__ss.__pc);
+    #else
+      error_addr = reinterpret_cast<void *>(uctx->uc_mcontext.pc);
+    #endif
 #elif defined(__mips__)
     error_addr = reinterpret_cast<void *>(
         reinterpret_cast<struct sigcontext *>(&uctx->uc_mcontext)->sc_pc);

You might wish to:

Apply this diff, or
Bump your version of backward-cpp to the latest release v1.6, which includes this patch

Cheers for Coot!
Blake

Use() called for unset Shader

Coot 1 (gtk3) emits the following diagnostic at startup:

GL ERROR:: --------------------------------- ooops Use() called for unset Shader

This appears to be coming from graphics_info_t::setup_draw_for_anchored_atom_markers_init(), and therefore to be related to graphics_info_t::shader_for_anchored_atom_markers. That is consistent with the absence of any call to that shader's init() method.

Screenshot not outputting

Now on

1.0.02 (revision-count 12068)
[with python 3.9.12 embedded]
git commit: 07fe2c3fd6389a7966a4bdb556566f8f7389cabc
Binary type: Darwin-MacOSX-12.3.1-x86_64gtk3

Trying to Draw > Screenshot > Simple

The popup window is fine. I get no warnings. After clicking OK, I see no output in the designated path.

Changed Shader settings to see if its because I was on Fancy and not plain. Made no difference

0.8.9.2 fails to build: no member named 'cout' in namespace 'std'

dynarama-main.cc:544:9: error: no member named 'cout' in namespace 'std'
   std::cout << "No goo canvas at compile-time, no dynarama " << std::endl;
   ~~~~~^
dynarama-main.cc:544:71: error: no member named 'endl' in namespace 'std'
   std::cout << "No goo canvas at compile-time, no dynarama " << std::endl;
                                                                 ~~~~~^
2 errors generated.

Did you forget to include <iostream>?

FreeBSD 11.2

This is a problem only when goocanvas isn't installed.

RDKit Atom::setMass() has been removed

When building with RDKit 2015_03_1 I get:

/home/wojdyr/checkout/coot-0.8.2/lidia-core/rdkit-interface.cc: In function ‘RDKit::RWMol coot::rdkit_mol(mmdb::Residue*, const coot::dictionary_residue_restraints_t&, const string&, bool)’:
/home/wojdyr/checkout/coot-0.8.2/lidia-core/rdkit-interface.cc:183:16: error: ‘class RDKit::Atom’ has no member named ‘setMass’
      rdkit_at->setMass(tbl->getAtomicWeight(atomic_number));
                ^
/home/wojdyr/checkout/coot-0.8.2/lidia-core/rdkit-interface.cc: In function ‘RDKit::RWMol coot::rdkit_mol(const coot::dictionary_residue_restraints_t&)’:
/home/wojdyr/checkout/coot-0.8.2/lidia-core/rdkit-interface.cc:604:7: error: ‘class RDKit::Atom’ has no member named ‘setMass’
   at->setMass(tbl->getAtomicWeight(atomic_number));

from RDKit changelog:

the method Atom::setMass() has been removed. Please use setIsotope() instead.

coot installation guide

How can I install this tool in Ubuntu v22.04? What is the best COOT installation guide? And how to access it?

Boost libraries and headers not found

While building Coot 1 on a machine that did not have Boost libraries or headers installed in the standard search paths, I found that configuring with --with-boost=/path/to/boost/headers --with-boost-libdir=/path/to/boost/libraries was not sufficient for a successful build. Some Coot components built successfully, which seems to show that I provided correct configuration options, but others did not see the boost headers and / or libraries. It looks like the needed flags variables were not inserted into the Makefile.am files in some of the places where they are needed.

This issue does not appear to be new, but it likely will not have manifested in build environments where Boost is installed in the standard search paths. It is potentially pernicious in such environments, however, for if a different Boost implementation than the default one is specified via configure arguments, such as the build-it script will do, then Coot can end up being built against a mixture of different Boost versions.

A pull request will be forthcoming soon.

build-it-3-3 failed

I checked out the gtk3 branch, commit aea798e
I then tried the autobuild using bash build-it-3-3, but the autobuild failed (log file attached below).

FYI, my OS is centos 7, I have installed cmake 3.23.1, and the centos equivalent packages (libxext-devel,libXt-devel,glibc-devel,mesa-libGLU-devel,gtk2-devel,libgnomecanvas-devel) specified in the INSTALL document.

Thanks!

================================================================
Fri Apr 22 13:35:39 PDT 2022
currently architecture is x86_64
dist is package fedora-release is not installed
dist is package redhat-release is not installed
dist is package redhat-release-workstation is not installed
dist is centos-release
systype: x86_64-centos-7
update_libtool: 1
update_config_guess_sub: 1
AUTOBUILD_BUILD=/home/sunch/autobuild/building
AUTOBUILD_INSTALLED=/home/sunch/autobuild/Linux-Pangu
AUTOBUILD_SOURCES=/home/sunch/autobuild/building/sources
BASH=/usr/bin/bash
BASHOPTS=cmdhist:extquote:force_fignore:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="0")
BASH_SOURCE=([0]="build-it-3-3")
BASH_VERSINFO=([0]="4" [1]="2" [2]="46" [3]="2" [4]="release" [5]="x86_64-redhat-linux-gnu")
BASH_VERSION='4.2.46(2)-release'
BINARY_INSTALL_CMD=www-placement
CBIN=/home/sunch/Programs/ccp4-7.0/bin
CCP4=/home/sunch/Programs/ccp4-7.0
CCP4I_TCLTK=/home/sunch/Programs/ccp4-7.0/bin
CCP4I_TOP=/home/sunch/Programs/ccp4-7.0/share/ccp4i
CCP4_HELPDIR=/home/sunch/Programs/ccp4-7.0/help/
CCP4_MASTER=/home/sunch/Programs
CCP4_OPEN=UNKNOWN
CCP4_SCR=/tmp/sunch
CCPEM=/home/sunch/Programs/ccpem-1.4.1
CETC=/home/sunch/Programs/ccp4-7.0/etc
CEXAM=/home/sunch/Programs/ccp4-7.0/examples
CHTML=/home/sunch/Programs/ccp4-7.0/html
CINCL=/home/sunch/Programs/ccp4-7.0/include
CLIB=/home/sunch/Programs/ccp4-7.0/lib
CLIBD=/home/sunch/Programs/ccp4-7.0/lib/data
CLIBD_MON=/home/sunch/Programs/ccp4-7.0/lib/data/monomers/
COLORTERM=truecolor
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/sunch/miniconda3/bin/conda
CONDA_PREFIX=/home/sunch/miniconda3
CONDA_PROMPT_MODIFIER='(base) '
CONDA_PYTHON_EXE=/home/sunch/miniconda3/bin/python
CONDA_SHLVL=1
CRANK=/home/sunch/Programs/ccp4-7.0/share/ccp4i/crank
CUDA_ROOT=/usr/local/cuda
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-wf6Nqb0Esc,guid=8fdbc6a58b156cb3d48d725f6247703a
DBUS_STARTER_ADDRESS=unix:abstract=/tmp/dbus-wf6Nqb0Esc,guid=8fdbc6a58b156cb3d48d725f6247703a
DBUS_STARTER_BUS_TYPE=session
DESKTOP_SESSION=gnome-classic
DIRSTACK=()
DISPLAY=:0
EUID=1000
FOR_DISABLE_STACK_TRACE=1
GDMSESSION=gnome-classic
GDM_LANG=en_US.UTF-8
GFORTRAN_UNBUFFERED_PRECONNECTED=Y
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GNOME_SHELL_SESSION_MODE=classic
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/2a2420aa_2a12_45fc_9eb8_3a679d3ee0ca
GNOME_TERMINAL_SERVICE=:1.116
GOPATH=/home/sunch/go
GROUPS=()
GSETTINGS_SCHEMA_DIR=/home/sunch/miniconda3/share/glib-2.0/schemas
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=
HISTCONTROL=ignoredups
HISTSIZE=1000
HOME=/home/sunch
HOST=Pangu
HOSTNAME=Pangu
HOSTTYPE=x86_64
IFS=$' \t\n'
IMOD_CALIB_DIR=/usr/local/ImodCalib
IMOD_DIR=/usr/local/IMOD
IMOD_JAVADIR=/usr/local/java
IMOD_PLUGIN_DIR=/usr/local/IMOD/lib/imodplug
IMOD_QTLIBDIR=/usr/local/IMOD/qtlib
IMSETTINGS_INTEGRATE_DESKTOP=yes
IMSETTINGS_MODULE=none
KDEDIRS=/usr
LANG=en_US.UTF-8
LESSOPEN='||/usr/bin/lesspipe.sh %s'
LIBTBX_BUILD=
LIBTBX_OPATH=
LIBTBX_TMPVAL=
LOADEDMODULES=
LOGNAME=sunch
LOGS=/home/sunch/public_html/build-logs/Linux-Pangu
LS_COLORS='rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:.tar=38;5;9:.tgz=38;5;9:.arc=38;5;9:.arj=38;5;9:.taz=38;5;9:.lha=38;5;9:.lz4=38;5;9:.lzh=38;5;9:.lzma=38;5;9:.tlz=38;5;9:.txz=38;5;9:.tzo=38;5;9:.t7z=38;5;9:.zip=38;5;9:.z=38;5;9:.Z=38;5;9:.dz=38;5;9:.gz=38;5;9:.lrz=38;5;9:.lz=38;5;9:.lzo=38;5;9:.xz=38;5;9:.bz2=38;5;9:.bz=38;5;9:.tbz=38;5;9:.tbz2=38;5;9:.tz=38;5;9:.deb=38;5;9:.rpm=38;5;9:.jar=38;5;9:.war=38;5;9:.ear=38;5;9:.sar=38;5;9:.rar=38;5;9:.alz=38;5;9:.ace=38;5;9:.zoo=38;5;9:.cpio=38;5;9:.7z=38;5;9:.rz=38;5;9:.cab=38;5;9:.jpg=38;5;13:.jpeg=38;5;13:.gif=38;5;13:.bmp=38;5;13:.pbm=38;5;13:.pgm=38;5;13:.ppm=38;5;13:.tga=38;5;13:.xbm=38;5;13:.xpm=38;5;13:.tif=38;5;13:.tiff=38;5;13:.png=38;5;13:.svg=38;5;13:.svgz=38;5;13:.mng=38;5;13:.pcx=38;5;13:.mov=38;5;13:.mpg=38;5;13:.mpeg=38;5;13:.m2v=38;5;13:.mkv=38;5;13:.webm=38;5;13:.ogm=38;5;13:.mp4=38;5;13:.m4v=38;5;13:.mp4v=38;5;13:.vob=38;5;13:.qt=38;5;13:.nuv=38;5;13:.wmv=38;5;13:.asf=38;5;13:.rm=38;5;13:.rmvb=38;5;13:.flc=38;5;13:.avi=38;5;13:.fli=38;5;13:.flv=38;5;13:.gl=38;5;13:.dl=38;5;13:.xcf=38;5;13:.xwd=38;5;13:.yuv=38;5;13:.cgm=38;5;13:.emf=38;5;13:.axv=38;5;13:.anx=38;5;13:.ogv=38;5;13:.ogx=38;5;13:.aac=38;5;45:.au=38;5;45:.flac=38;5;45:.mid=38;5;45:.midi=38;5;45:.mka=38;5;45:.mp3=38;5;45:.mpc=38;5;45:.ogg=38;5;45:.ra=38;5;45:.wav=38;5;45:.axa=38;5;45:.oga=38;5;45:.spx=38;5;45:.xspf=38;5;45:'
MACHTYPE=x86_64-redhat-linux-gnu
MAIL=/var/spool/mail/sunch
MMCIFDIC=/home/sunch/Programs/ccp4-7.0/lib/ccp4/cif_mmdic.lib
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
MODULESHOME=/usr/share/Modules
NIGHTLY_DEST_DIR=/home/sunch/public_html/software/binaries/nightlies/pre-release
OPTERR=1
OPTIND=1
OS=Linux
OSTYPE=linux-gnu
PATH=/home/sunch/autobuild/Linux-Pangu-pre-release-gtk3/bin:/usr/local/phenix-1.20.1-4487/build/bin:/home/sunch/bin:/home/sunch/Programs/cistem-1.0.0-beta:/home/sunch/Documents/git-projects/relion/build/bin:/home/sunch/Programs/ccpem-1.4.1/bin:/home/sunch/Programs/ccp4-7.0/etc:/home/sunch/Programs/ccp4-7.0/bin:/home/sunch/miniconda3/bin:/home/sunch/miniconda3/condabin:/usr/local/IMOD/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/cuda/bin:/home/sunch/.local/UCSF-Chimera64-1.14/bin:/home/sunch/.local/bin:/home/sunch/Programs/frealign_v9.11/bin:/home/sunch/Programs/julia-1.6.1/bin:/home/sunch/Downloads/Situs_3.1/bin:/home/sunch/Downloads/MAINMAST:/home/sunch/Programs/cryoEF_v1.1.0/bin:/home/sunch/Programs/hole2/hole2/exe:/usr/local/go/bin:/home/sunch/Programs/frealign_v9.11/bin:/home/sunch/Programs/julia-1.6.1/bin:/home/sunch/Downloads/Situs_3.1/bin:/home/sunch/Downloads/MAINMAST:/home/sunch/Programs/cryoEF_v1.1.0/bin:/home/sunch/Programs/hole2/hole2/exe:/usr/local/go/bin:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc
PHENIX=/usr/local/phenix-1.20.1-4487
PHENIX_VERSION=1.20.1-4487
PIPESTATUS=([0]="1")
PPID=9554
PS4='+ '
PWD=/home/sunch/Documents/git-projects/coot
QT_GRAPHICSSYSTEM_CHECKED=1
QT_IM_MODULE=ibus
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
ROSETTA3=/home/sunch/Programs/rosetta_bin_linux_2020.08.61146_bundle/main/source
ROSETTA3_DB=/home/sunch/Programs/rosetta_bin_linux_2020.08.61146_bundle/main/database
ROSETTA3_TOOLS=/home/sunch/Programs/rosetta_bin_linux_2020.08.61146_bundle/main/tools
SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/4646,unix/unix:/tmp/.ICE-unix/4646
SHELL=/bin/bash
SHELLOPTS=braceexpand:hashall:interactive-comments
SHLVL=3
SSH_AGENT_PID=4784
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
SSL_CERT_FILE=/home/sunch/Programs/ccp4-7.0/etc/ssl/cacert.pem
STABLE_DEST_DIR=/home/sunch/public_html/software/binaries/stable
TERM=xterm-256color
UID=1000
USER=sunch
USERNAME=sunch
VTE_VERSION=5202
WINDOWPATH=1
XAUTHORITY=/run/gdm/auth-for-sunch-seRIMY/database
XDG_CURRENT_DESKTOP=GNOME-Classic:GNOME
XDG_DATA_DIRS=/home/sunch/.local/share/flatpak/exports/share/:/var/lib/flatpak/exports/share/:/usr/local/share/:/usr/share/
XDG_MENU_PREFIX=gnome-
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT=seat0
XDG_SESSION_DESKTOP=gnome-classic
XDG_SESSION_ID=3
XDG_SESSION_TYPE=x11
XDG_VTNR=1
XMODIFIERS=@im=ibus
_=']'
_CE_CONDA=
_CE_M=
arch=x86_64
architecture=x86_64
build_coot_prerelease=1
build_type=gtk3
dist=centos-release
dist_name=centos
dist_ver=7
do_nightlies=1
fallback_coot_version=coot-0.4
gtk_version=3
have_malloc=1
i=centos-release
no_proxy=.corp.net.com
processor=GNU/Linux
proxy_host=myproxy.com
proxy_port=800
publish=:
publish_logs=:
run_second_test=true
run_tests=false
script_version=6.02
shared_lib_ext=so
shared_static_flag=--disable-static
specs=/home/sunch/autobuild/build-scripts/Pangu-specials
systype=x86_64-centos-7
update_config_guess_sub=1
update_libtool=1
use_proxy=
fixup_libcurl ()
{
sed s,-L/usr/lib,, curl-config > curl-config.tmp;
mv curl-config.tmp curl-config;
sed s,-L/usr/lib,, lib/libcurl.la > lib/libcurl.la.tmp;
mv lib/libcurl.la.tmp lib/libcurl.la
}
make_tar ()
{
echo in make_tar args: $1 $2;
echo in make_tar: in dir: $PWD;
tar_dir=$1;
tar_file_name=$2;
cd $install_top_dir/..;
if [ -e $tar_dir ]; then
echo taring nightly... from $tar_dir to $tar_file_name;
tar czf $tar_file_name $tar_dir;
status=$?;
if [ "$status" != 0 ]; then
echo ERROR:: tar czf $tar_file_name $tar_dir failed.;
echo ERROR:: while in directory $(pwd);
echo ERROR:: tar failed > $tar_file_name.md5sum;
rm $tar_file_name;
else
md5sum $tar_file_name > $tar_file_name.md5sum;
/bin/ls -l $tar_file_name >> $tar_file_name.md5sum;
echo done tar successfully.;
fi;
else
echo ERROR:: tar target directory $tar_dir does not exist.;
fi
}
mkdir_maybe ()
{
dir=$1;
if [ ! -e "$dir" ]; then
mkdir $dir;
fi
}
module ()
{
eval /usr/bin/modulecmd bash $*
}
my_exit ()
{
exit_arg=$1;
shift;
extra_args=$;
echo fail-build $extra_args > $LOGS/$build-status;
if [ -e $LOGS/$test-status ]; then
rm $LOGS/$test-status;
fi;
exit $exit_arg
}
post_install_slim ()
{
echo we are slimming directory $1;
fat_dir="$1";
cleaned_dir="$2";
clear_type="$3";
echo fat_dir is $fat_dir;
echo clear_type is $clear_type;
echo cleaned_dir is $cleaned_dir;
mkdir_maybe $cleaned_dir;
mkdir_maybe $cleaned_dir/bin;
mkdir_maybe $cleaned_dir/lib;
if [ "$ENABLE_PYTHON_COOT" = yes ]; then
mkdir_maybe $cleaned_dir/include;
mkdir_maybe $cleaned_dir/include/$python_version;
fi;
lib_sos=cd $fat_dir && ls -1 lib/lib*.so*;
lib_as=cd $fat_dir && ls -1 lib/lib*.a;
if [ "$clear_type" = "clear-dynamic" ]; then
keep_lib_archs="$lib_as";
fi;
if [ "$clear_type" = "clear-static" ]; then
keep_lib_archs="$lib_sos";
fi;
file_list="etc info man share libexec libexec/coot-bin libexec/findwaters-bin libexec/findligand-bin libexec/mini-rsr-bin libexec/density-score-by-residue-bin bin/coot bin/findwaters bin/findligand bin/guile bin/coot-density-score-by-residue bin/coot-available-comp-id bin/coot-compare-dictionaries bin/coot-make-shelx-restraints bin/coot-dictionary-bond-distributions bin/lidia bin/curl $keep_lib_archs";
if [ "$ENABLE_PYTHON_COOT" = yes ]; then
file_list="$file_list html lib/$python_version include/$python_version";
fi;
echo rsyncing...;
for file in $file_list;
do
dn=$(dirname $file);
if [ -e $fat_dir/$file ]; then
rsync -axr $fat_dir/$file $cleaned_dir/$dn;
else
echo $fat_dir/$file does not exist;
fi;
done;
echo done rsyncing.
}
setup_ccp4 ()
{
if test "$OS" = Linux; then
setup_file=/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/include/ccp4.setup-sh;
if test -e $setup_file; then
. $setup_file;
else
if [ "$systype" = x86_64-centos-6 ]; then
setup_file=/home/emsley/ccp4/setup-scripts/sh/ccp4.setup;
else
if [ "$systype" = x86_64-centos-5 ]; then
setup_file=/home/emsley/ccp4/ccp4-6.2.0/include/ccp4.setup-sh;
else
setup_file=setup-ccp4;
fi;
fi;
if test -e $setup_file; then
echo evaluating $setup_file;
. $setup_file;
else
echo WARNING:: ccp4 setup file $setup_file does not exist.;
fi;
fi;
fi;
if test "$OS" = Darwin; then
. /usr/local/ccp4-6.0.2/bin/ccp4.setup-sh;
fi
}
ssh_copy ()
{
if [ "$do_ssh_copy" = true ]; then
dir=public_html/software/binaries/nightlies/pre-release/;
echo ssh_copy copying over files using $HOME/bin/sput-with-dir $bin_tar_file $dir;
$HOME/bin/sput-with-dir $bin_tar_file $dir;
if [ -e $bin_tar_file.md5sum ]; then
$HOME/bin/sput-with-dir $bin_tar_file.md5sum dir;
fi;
else
echo Not ssh copying file to York, $domainname;
fi
}
ssh_copy_logs_to_biop ()
{
local_log_dir=$1;
target_dir=$2;
if [ "$do_ssh_biop_copy" = true ]; then
echo copying over log files to Biop...;
target_dir=$2;
$HOME/bin/sput-with-dir $local_log_dir $target_dir;
else
echo Not ssh copying log files to biop;
fi
}
ssh_copy_to_biop ()
{
bin_tar_file=$1;
if [ "$do_ssh_biop_copy" = true ]; then
target_dir=public_html/coot/software/binaries/pre-releases/;
echo copying over files to Biop: $HOME/bin/sput-with-dir $bin_tar_file $target_dir;
$HOME/bin/sput-with-dir $bin_tar_file $target_dir;
if [ -e $bin_tar_file.md5sum ]; then
echo and also: $HOME/bin/sput-with-dir $bin_tar_file.md5sum $target_dir;
$HOME/bin/sput-with-dir $bin_tar_file.md5sum $target_dir;
fi;
else
echo Not ssh copying file to biop;
fi
}
test_coot ()
{
echo testing with greg;
echo testing with greg 1>&2;
echo currently we are here:;
pwd;
date;
if [ "$1" != "" ]; then
coot_binary=$1;
else
coot_binary=$install_top_dir/libexec/coot-bin;
fi;
if test "$run_tests" = true; then
COOT_PYTHON_DIR=$install_top_dir/share/coot/python;
PYTHONPATH=$COOT_PYTHON_DIR;
PYTHONHOME=$install_top_dir;
export COOT_PYTHON_DIR;
export PYTHONPATH;
export PYTHONHOME;
if [ ! -d greg-tests ]; then
echo greg-tests dir missing in this directory:;
pwd;
return 1;
fi;
setup_ccp4;
cat > command-line-greg.scm <<EOF
(use-modules (ice-9 greg))
(set! greg-tools (list "greg-tests"))
(set! greg-debug #t)
(set! greg-verbose 5)
(let ((r (greg-test-run)))
(if r
(coot-real-exit 0)
(coot-real-exit 1)))
EOF

    echo $install_top_dir/bin/coot --no-graphics --script command-line-greg.scm;
    $install_top_dir/bin/coot --no-graphics --script command-line-greg.scm;
    status=$?;
    if [ $status = 0 ]; then
        echo test_coot: coot test passed;
        return 0;
    else
        echo test_coot: coot test failed;
        return 1;
    fi;
else
    echo run_tests is not true, not testing.;
    return 1;
fi

}
test_coot_python ()
{
echo testing with python unittest;
echo testing with python unittest 1>&2;
echo currently we are here:;
pwd;
if test "$run_tests" = true; then
COOT_PYTHON_DIR=$install_top_dir/share/coot/python;
PYTHONPATH=$COOT_PYTHON_DIR;
PYTHONHOME=$install_top_dir;
export COOT_PYTHON_DIR;
export PYTHONPATH;
export PYTHONHOME;
echo $install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py;
$install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py;
status=$?;
if [ $status = 0 ]; then
echo test_coot_python: coot test passed;
return 0;
else
echo test_coot_python: coot test failed;
return 1;
fi;
else
return 1;
fi
}
INFO:: MACHTYPE is x86_64-redhat-linux-gnu
INFO:: systype is x86_64-centos-7
g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

new version path
need_guile_unused_values_patch is true
Testing version of make
GNU Make 3.82
Built for x86_64-redhat-linux-gnu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
using 8 processors in compilation
MAKE set to make -j8
testing for patch
testing awk type (prefer GNU awk)
GNU Awk 4.0.2
Copyright (C) 1989, 1991-2012 Free Software Foundation.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program. If not, see http://www.gnu.org/licenses/.
good, you have an awk from GNU.
cmake version 3.23.1 CMake suite maintained and supported by Kitware (kitware.com/cmake).
found recent cmake
cmake_is_good: true
cmake passes
start_dir /home/sunch/Documents/git-projects/coot
Date: 2022-04-22__T20_35_39
pkg-config is /usr/bin/pkg-config
pkg-config is new enough 0.27.1
checking wget
which wget
/usr/bin/wget
pre_release_files_html /home/sunch/autobuild/building/sources/index-pre-release.html
coot_version_tmp : :
clever coot_version extraction failed, using default.
debug:: wget -P /home/sunch/autobuild/building/sources -O /home/sunch/autobuild/building/sources/index.html -o /home/sunch/autobuild/building/sources/wget-e.s.p.log http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/pre-releases/
INFO:: building pre-release and coot_version_pre is
trying to build pre-release coot, but failed to find pre-release version
make a stable release then
examining release server files /home/sunch/autobuild/building/sources/index.html
coot_version
INFO:: binary tar destination dir: BINARY_TAR_DEST_DIR is /home/sunch/public_html/software/binaries/stable
INFO:: coot_version_pre is
INFO:: build_coot_prerelease is
INFO:: release_server_dir is http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases
INFO:: coot_version is
INFO:: build_type is gtk3
python_libs is LIBS=-L/home/sunch/autobuild/Linux-Pangu-gtk3/lib64
install_top_dir /home/sunch/autobuild/Linux-Pangu-gtk3
COOT_CCP4_PACKAGES
PKG_CONFIG_PATH is now /home/sunch/autobuild/Linux-Pangu-gtk3/lib64/pkgconfig:/home/sunch/autobuild/Linux-Pangu-gtk3/lib/pkgconfig:/home/sunch/autobuild/Linux-Pangu-gtk3/lib/x86_64-linux-gnu/pkgconfig:/lib/pkgconfig
system/installation has freetype2
glib is not up to date, rebuild glib - maybe.
testing for install_top_dir: /home/sunch/autobuild/Linux-Pangu-gtk3
INFO:: /home/sunch/autobuild/Linux-Pangu-gtk3 exists already.
done testing for /home/sunch/autobuild/Linux-Pangu-gtk3
ccp4_system_type linux
installation has fftw
installation has curl/libcurl
installation does not have libidn2, libcurl should be built also
libtool test: looking for /home/sunch/autobuild/Linux-Pangu-gtk3/include/ltdl.h
/home/sunch/autobuild/Linux-Pangu-gtk3/include/ltdl.h
installation has libtool
/home/sunch/autobuild/Linux-Pangu-gtk3
system/installation has the GSL version 1.16
build_gsl is 0
GSL is up to date
SSM is found.
INFO:: shall we build clipper: mmdb not to be built
INFO:: shall we build clipper: fftw not to be built
Python 3.9.12
we have python3
not building libccp4:
not building mmdb:
not building ssm:
not building fftw:
not building clipper:
BUILDING readline:
ffi build - testing existance /home/sunch/autobuild/Linux-Pangu-gtk3/lib/libffi-3.2.1/include/fffi.h
/home/sunch/autobuild/Linux-Pangu-gtk3/lib/libffi-3.2.1/include does not exist
BUILDING libffi 3.2.1:
not building python:
0.61.2
we have meson
not building meson
not building glib:
BUILDING gobject-introspection:
installation has pycairo
BUILDING pygobject:
Fri Apr 22 13:35:56 PDT 2022
/home/sunch/autobuild/building/Pangu_2022-04-22__T20_35_39
BUILDING pygobject 3.36.1:
not building gmp:
not building libtool:
BUILDING libidn:
BUILDING curl:
not building gsl:
not building boost
not building Raster3D render
not building glm
installing pygobject with pip3
pip3 install --upgrade pip
Requirement already satisfied: pip in /home/sunch/autobuild/Linux-Pangu-gtk3/lib/python3.9/site-packages (22.0.4)
pip3 install cython
Requirement already satisfied: cython in /home/sunch/autobuild/Linux-Pangu-gtk3/lib/python3.9/site-packages (0.29.28)
-rw-r--r--. 1 sunch sunch 4855 Apr 21 16:09 /home/sunch/autobuild/Linux-Pangu-gtk3/lib/python3.9/site-packages/numpy-1.19.4-py3.9-linux-x86_64.egg/numpy/lib/_version.py
numpy is found, skip
not building rdkit:
building QED
libunistring skip_this true
not building libunistring
not building gc
not building gmp
BUILDING guile:
BUILDING g-wrap:
BUILDING guile-cairo
guile-lib needs to be installed
some test here
guile-config found
guile-gnome-platform skip_this false
222222222222222 Now Coot.....
Fri Apr 22 13:36:46 PDT 2022
/home/sunch/Documents/git-projects/coot
BUILDING coot
coot build failed, exiting.

png support missing for windows (testing this thing here)

png-libs not found by default on windows, so USE_LIBPNG has no effect
we dont get a screen shot on windows

Original issue reported on code.google.com by [email protected] on 19 Jan 2010 at 12:40

Rama HUD not interactive?

Hi @pemsley,

I really like the new local Ramachandran overlay during RSR! Would it be possible to make the plot interactive, so we can click on and navigate to outliers? Or is it supposed to be like that already but not working on Mac yet?

Cheers
Oli

the configure script do not fail if swig is not available

Hello,

without swig the configure process run without error
but make gives this error

make[1]: entrant dans le répertoire « /home/picca/Projets/coot/src »
swig -o coot_wrap_guile_pre_gtk2.cc -DCOOT_USE_GTK2_INTERFACE  
-DHAVE_SYS_STDTYPES_H=0   -DUSE_LIBCURL -I../src -guile -c++  ../src/coot.i
/bin/bash: swig : commande introuvable


so it seems that swig is mendatory.
Can you teach configure.in to fail if swig is not available or do not compile 
the swig code if it is not available.

thanks

Frederic

Original issue reported on code.google.com by [email protected] on 13 Jan 2013 at 7:05

Request - show nearby residues when selecting residue in Ramachandran plot

Hi Paul, when navigating the main Ramachandran plot interface, clicking on a residue recenters on that residue. It would be useful if there were a way to then see just which residues (general or outliers) are nearby in either sequence or 3D space. The rama HUD does this during refinement, but it would be useful to have access to a similar tool outside of refinement when identifying problem regions.

Also, is there any possibility of flagging "dubious" residues on the ramachandran? Not outliers per se but outliers given structural context. E.g., a residue in the middle of a helix that has "allowed" but non helical phi/psi...?

Cheers
Oli

renumber residue panel is missing chain selection

The Renumber Residue panel is missing:
-dropdown menu for the chain
-the ability to specify the terminal residue to which the range should apply to

infinite stream of "INFO:: found bad THR chiral atom" messages

I downloaded 4q4w from pdb and expanded it using iotbx.pdb.expand_ncs.

$ coot 4q4w_ncs.pdb
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /home/wojdyr/ccp4/ccp4-linux64-2016-05-17-0115/lib/data/monomers/
INFO:: Reading coordinate file: /home/wojdyr/ccp4/ccp4-linux64-2016-05-17-0115/share/coot/standard-residues.pdb
 PDB file /home/wojdyr/ccp4/ccp4-linux64-2016-05-17-0115/share/coot/standard-residues.pdb has been read.
Spacegroup: P 1
initalize graphics molecules...done.
^[[1m(filter-fileselection-filenames-state)^[[0m
^[[1m(get-active-map-drag-flag)^[[0m
^[[1m(use-graphics-interface-state)^[[0m
INFO:: coot.py imported

** (coot-bin:20379): WARNING **: Trying to register gtype 'GMountMountFlags' as enum when in fact it is of type 'GFlags'

** (coot-bin:20379): WARNING **: Trying to register gtype 'GDriveStartFlags' as enum when in fact it is of type 'GFlags'

** (coot-bin:20379): WARNING **: Trying to register gtype 'GSocketMsgFlags' as enum when in fact it is of type 'GFlags'
INFO:: coot_python initialized
Running python script /home/wojdyr/ccp4/ccp4-linux64-2016-05-17-0115/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Evening Wojdyr, Welcome to Coot. 0.8.3
^[[1m(set-display-intro-string "Good Evening Wojdyr, Welcome to Coot. 0.8.3")^[[0m
Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
^[[1m(use-graphics-interface-state)^[[0m
^[[1m(filter-fileselection-filenames-state)^[[0m
^[[1m(get-active-map-drag-flag)^[[0m
^[[1m(use-graphics-interface-state)^[[0m
Coot Scheme Scripting GUI code found and loaded.
^[[1m(set-display-intro-string "Good evening ,,,. Welcome to Coot")^[[0m
^[[1m(set-display-lists-for-maps 0)^[[0m
^[[1m(handle-read-draw-molecule-with-recentre "4q4w_ncs.pdb" 1)^[[0m
INFO:: Reading coordinate file: 4q4w_ncs.pdb
 PDB file 4q4w_ncs.pdb has been read.
Spacegroup: I 2 2 2
INFO:: Found 1 models
   Model 1 had 0 links
Symmetry available for this molecule
INFO:: NCS chain comparison 14/582
INFO:: NCS chain comparison 6/582
INFO:: NCS chain comparison 3/582
INFO:: NCS chain comparison 156/507
INFO:: NCS chain comparison 3/507
INFO:: NCS chain comparison 2/453
Molecule 0 read successfully
DEBUG:: there were 3 types with no dictionary
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB
INFO:: found bad THR chiral atom: 1 26   CB

and so on. Coot window is not responding.
The output is perhaps finite, I killed it after waiting a couple minutes.

Compiling Coot

when I run ./configure, Ifix the all error.
Then I type make , the error is up:
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DPACKAGE_NAME="coot" -DPACKAGE_TARNAME="coot" -DPACKAGE_VERSION="1.0.02" -DPACKAGE_STRING="coot\ 1.0.02" -DPACKAGE_BUGREPORT="" -DPACKAGE_URL="" -DPACKAGE="coot" -DVERSION="1.0.02" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=".libs/" -DHAVE_OPENMP=1 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_PYTHON="3.8" -DHAVE_BOOST=/**/ -DHAVE_BOOST_PYTHON=/**/ -I. -g -O2 -Wall -Wno-unused -std=c++11 -c -o getopt.lo getopt.cc
/bin/bash: ../depcomp: No such file or directory
make[1]: *** [Makefile:547: getopt.lo] Error 127
make[1]: Leaving directory '/home/paul/Documents/coot-1.0.02/compat'
make: *** [Makefile:723: all-recursive] Error 1

could you give me some ideas? Thanks so much!

Problem with Hombrew install script for intel macs (M1's work fine)

Many thanks for the work that has been done on this.

Whilst the homebrew install script completes for both intel and M1 processors when coot is opened on an intel machine it throws the following errors.

WARNING:: validation failed: model-as-mesh.shader validation status 0
GL ERROR:: Shader::Use() "model-as-mesh.shader" err 1282 for program_id 94
GL ERROR:: set_uniform_locations() error 1: 1282
GL ERROR:: set_uniform_locations() error 2: 1282
GL ERROR:: set_uniform_locations() error 3: 1282
GL ERROR:: set_uniform_locations() error 4: 1282
Shader compile               model-as-mesh.shader validation-failed

And

GL ERROR:: Shader::set_int_for_uniform() "screen.shader" B glUniform1i for uniform screenTexture loc: 1 value: 0 err 1282
GL ERROR:: Shader::set_int_for_uniform() "screen.shader" B glUniform1i for uniform screenDepth loc: 2 value: 1 err 1282
GL ERROR:: Shader::set_int_for_uniform() "blur.shader" B glUniform1i for uniform screenTexture loc: 4 value: 0 err 1282
GL ERROR:: Shader::set_int_for_uniform() "blur.shader" B glUniform1i for uniform screenDepth loc: 5 value: 1 err 1282

This results in a marked reduction in performance for coot running on intel Mac's.

coot-1 build fail

Running the build-it-3-3 script to compile coot-1, this error occurs:

             from ../../coot/src/init_coot_as_python_module.cc:12:
../../coot/src/Mesh.hh:10:10: fatal error: g_triangle.hh: No such file or directory
#include "g_triangle.hh"
^~~~~~~~~~~~~~~
compilation terminated.
Makefile:2067: recipe for target 'init_coot_as_python_module.lo' failed
make[1]: *** [init_coot_as_python_module.lo] Error 1
make[1]: Leaving directory '/scratch/download/coot/build-coot/src'
Makefile:723: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1
make failed.

g_triangle.hh does not seem to be in the source code?

Build failure: ‘gtk_combo_box_get_active_text’ was not declared in this scope

I'm trying to build Coot 1 on CentOS Stream 8, using (mostly) the system libraries. In particular, I am using the system's GTK+ 3, version 3.22.30. Coot's configure script finds GTK3 just fine, and it puts what appears to be the correct -I flag for that into the compilation command:
libtool: compile: g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"1\" "-DPACKAGE_STRING=\"coot 1\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_PYTHON=\"3.6\" "-DHAVE_BOOST=/**/" "-DHAVE_BOOST_PYTHON=/**/" -I. -DUSE_PYTHON -I.. -I/usr/include -I/usr/include/goocanvas-2.0 -I/usr/include/gtk-3.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/uuid -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/atk-1.0 -I/usr/include/at-spi2-atk/2.0 -I/usr/include/at-spi-2.0 -I/usr/include/dbus-1.0 -I/usr/lib64/dbus-1.0/include -pthread -I/usr/include/gtk-3.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/uuid -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/atk-1.0 -I/usr/include/at-spi2-atk/2.0 -I/usr/include/at-spi-2.0 -I/usr/include/dbus-1.0 -I/usr/lib64/dbus-1.0/include -pthread -I/opt/ccp4/ccp4-7.1/include -DCLIPPER_HAS_TOP8000 -DHAVE_CCP4SRS -I/opt/ccp4/ccp4-7.1/include -I/opt/ccp4/ccp4-7.1/include -DMMDB_HAS_LINK_DISTANCE -DMAKE_ENHANCED_LIGAND_TOOLS -I/usr/include/rdkit -DRDKIT_HAS_CAIRO_SUPPORT -I/usr/include -I/usr/include/python3.6m -DPKGDATADIR=\"/usr/local/share/coot\" -g -O2 -Wall -Wno-unused -Wmissing-prototypes -Wmissing-declarations -Wshadow -Woverloaded-virtual -std=c++11 -MT lbg-search.lo -MD -MP -MF .deps/lbg-search.Tpo -c lbg-search.cc -fPIC -DPIC -o .libs/lbg-search.o

Nevertheless, the build fails:

lbg-search.cc: In member function ‘double lbg_info_t::get_search_similarity() const’:
lbg-search.cc:214:17: error: ‘gtk_combo_box_get_active_text’ was not declared in this scope
    gchar *txt = gtk_combo_box_get_active_text(GTK_COMBO_BOX(lbg_search_combobox));
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Function gtk_combo_box_get_active_text() has been deprecated since GTK+ 2.24, but apparently it has now been removed altogether, at least from some builds. The GTK 2 docs provide some recommendations for replacements.

the dist target is not working.

Hello, to prepare the release of coot you will need to run

make distcheck

but with the current svn this target is failling.

make[1]: Entering directory `/home/picca/Projets/coot/src'
make[1]: *** No rule to make target `svn-revision.cc', needed by `distdir'.  
Stop.
make[1]: Leaving directory `/home/picca/Projets/coot/src'
make: *** [distdir] Error 1

cheers

frederic.


PS: I am preparing a Debian package for coot. so I am trying to stay as close 
as possible to the current svn.

Original issue reported on code.google.com by [email protected] on 12 Jan 2013 at 4:50

$HOME/python-3.8/lib/python3.8/site-packages/PyGObject-3.36.1-py3.8-macosx-11.5-x86_64.egg/include added to include path

harmless(?). Due to:

coot/src/Makefile.am

Line 214 in 07fe2c3

    
           PYGOBJECT_CFLAGS=-I$(HOME)/python-3.8/lib/python3.8/site-packages/PyGObject-3.36.1-py3.8-macosx-11.5-x86_64.egg/include

1.0.02 crashes while loading an mrc file

Hi,
I have compiled version 1.0.02 but I'm seeing some startup errors on my system and the coot program crashes when I try to open an map/mrc file. The messages from the startup and the crash happens just as I open the mrc file. I can provide a core file, if that is helpful.
Regards,
Jeff

$ coot
Fatal Python error: Py_Initialize: can't initialize sys standard streams
Traceback (most recent call last):
File "/usr/lib64/python3.9/abc.py", line 85, in
ModuleNotFoundError: No module named '_abc'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/lib64/python3.9/io.py", line 52, in
File "/usr/lib64/python3.9/abc.py", line 89, in
File "/usr/lib64/python3.9/_py_abc.py", line 35
def new(mcls, name, bases, namespace, /, **kwargs):
^
SyntaxError: invalid syntax
Fatal Python error: Py_Initialize: can't initialize sys standard streams
Traceback (most recent call last):
File "/usr/lib64/python3.9/abc.py", line 85, in
ModuleNotFoundError: No module named '_abc'

During handling of the above exception, another exception occurred:

(coot-bin:2364677): Gtk-CRITICAL **: 10:31:28.411: gtk_menu_item_set_submenu: assertion 'GTK_IS_MENU_ITEM (menu_item)' failed
DEBUG:: setting OpenGL required version to 3 3
OOPS:: on_glarea_realize() error on gtk_gl_area_make_current()
Coot Python Scripting GUI code found and loaded.

(coot-bin:2364677): Gtk-CRITICAL **: 10:31:42.555: gtk_widget_grab_default: assertion 'gtk_widget_get_can_default (widget)' failed
Gtk-Message: 10:31:42.555: GtkDialog mapped without a transient parent. This is discouraged.
INFO:: map file type was determined to be CCP4 type
DEBUG:: init xmap with P 1 Cell (633597,633597, 0, 90, 90, 90) Nuvw = (2048,2048, 1)
/panfs/hisoftware/cryoem/coot/1.0.02/bin/coot: line 229: 2364677 Segmentation fault (core dumped) $coot_bin "$@"
. ------ Coot crashed - trying to diagnose -----

run make error PyObject not yet declared in this scope

when I built coot-0.8.9.1, I got this.

cc-interface-image.hh:5:32: 错误：‘PyObject’在此作用域中尚未声明
    5 | std::string text_png_as_string(PyObject *text_info_dict);
      |                                ^~~~~~~~
In file included from /usr/include/gtk-2.0/gtk/gtk.h:89,
                 from globjects.cc:42:
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:59:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   59 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:60:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   60 |   void (*__gtk_reserved2);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:61:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved3’ [-Wparentheses]
   61 |   void (*__gtk_reserved3);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:62:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved4’ [-Wparentheses]
   62 |   void (*__gtk_reserved4);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:63:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved5’ [-Wparentheses]
   63 |   void (*__gtk_reserved5);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:64:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved6’ [-Wparentheses]
   64 |   void (*__gtk_reserved6);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:65:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved7’ [-Wparentheses]
   65 |   void (*__gtk_reserved7);
      |        ^
cc-interface-image.hh:5:42: 错误：‘text_info_dict’在此作用域中尚未声明
    5 | std::string text_png_as_string(PyObject *text_info_dict);
      |                                          ^~~~~~~~~~~~~~
In file included from /usr/include/gtk-2.0/gtk/gtk.h:173,
                 from globjects.cc:42:
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:76:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   76 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:77:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   77 |   void (*__gtk_reserved2);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:89,
                 from graphics-info.h:37,
                 from globularize.cc:6:
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:59:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   59 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:60:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   60 |   void (*__gtk_reserved2);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:61:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved3’ [-Wparentheses]
   61 |   void (*__gtk_reserved3);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:62:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved4’ [-Wparentheses]
   62 |   void (*__gtk_reserved4);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:63:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved5’ [-Wparentheses]
   63 |   void (*__gtk_reserved5);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:64:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved6’ [-Wparentheses]
   64 |   void (*__gtk_reserved6);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:65:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved7’ [-Wparentheses]
   65 |   void (*__gtk_reserved7);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:173,
                 from graphics-info.h:37,
                 from globularize.cc:6:
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:76:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   76 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:77:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   77 |   void (*__gtk_reserved2);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:89,
                 from graphics-info.h:37,
                 from graphics-info-defines.cc:36:
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:59:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   59 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:60:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   60 |   void (*__gtk_reserved2);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:61:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved3’ [-Wparentheses]
   61 |   void (*__gtk_reserved3);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:62:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved4’ [-Wparentheses]
   62 |   void (*__gtk_reserved4);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:63:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved5’ [-Wparentheses]
   63 |   void (*__gtk_reserved5);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:64:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved6’ [-Wparentheses]
   64 |   void (*__gtk_reserved6);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:65:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved7’ [-Wparentheses]
   65 |   void (*__gtk_reserved7);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:173,
                 from graphics-info.h:37,
                 from graphics-info-defines.cc:36:
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:76:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   76 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:77:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   77 |   void (*__gtk_reserved2);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:89,
                 from graphics-info-graphs.cc:42:
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:59:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   59 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:60:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   60 |   void (*__gtk_reserved2);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:61:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved3’ [-Wparentheses]
   61 |   void (*__gtk_reserved3);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:62:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved4’ [-Wparentheses]
   62 |   void (*__gtk_reserved4);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:63:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved5’ [-Wparentheses]
   63 |   void (*__gtk_reserved5);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:64:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved6’ [-Wparentheses]
   64 |   void (*__gtk_reserved6);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:65:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved7’ [-Wparentheses]
   65 |   void (*__gtk_reserved7);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:89,
                 from graphics-info.cc:41:
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:59:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   59 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:60:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   60 |   void (*__gtk_reserved2);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:61:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved3’ [-Wparentheses]
   61 |   void (*__gtk_reserved3);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:62:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved4’ [-Wparentheses]
   62 |   void (*__gtk_reserved4);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:63:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved5’ [-Wparentheses]
   63 |   void (*__gtk_reserved5);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:64:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved6’ [-Wparentheses]
   64 |   void (*__gtk_reserved6);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:65:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved7’ [-Wparentheses]
   65 |   void (*__gtk_reserved7);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:173,
                 from graphics-info-graphs.cc:42:
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:76:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   76 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:77:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   77 |   void (*__gtk_reserved2);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:173,
                 from graphics-info.cc:41:
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:76:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   76 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:77:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   77 |   void (*__gtk_reserved2);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:89,
                 from graphics-info-gui.cc:42:
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:59:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   59 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:60:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   60 |   void (*__gtk_reserved2);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:61:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved3’ [-Wparentheses]
   61 |   void (*__gtk_reserved3);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:62:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved4’ [-Wparentheses]
   62 |   void (*__gtk_reserved4);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:63:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved5’ [-Wparentheses]
   63 |   void (*__gtk_reserved5);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:64:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved6’ [-Wparentheses]
   64 |   void (*__gtk_reserved6);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:65:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved7’ [-Wparentheses]
   65 |   void (*__gtk_reserved7);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:173,
                 from graphics-info-gui.cc:42:
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:76:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   76 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:77:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   77 |   void (*__gtk_reserved2);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:89,
                 from cc-interface.hh:26,
                 from cc-interface-png.cc:27:
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:59:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   59 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:60:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   60 |   void (*__gtk_reserved2);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:61:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved3’ [-Wparentheses]
   61 |   void (*__gtk_reserved3);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:62:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved4’ [-Wparentheses]
   62 |   void (*__gtk_reserved4);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:63:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved5’ [-Wparentheses]
   63 |   void (*__gtk_reserved5);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:64:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved6’ [-Wparentheses]
   64 |   void (*__gtk_reserved6);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:65:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved7’ [-Wparentheses]
   65 |   void (*__gtk_reserved7);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:89,
                 from graphics-info-modelling.cc:45:
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:59:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   59 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:60:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   60 |   void (*__gtk_reserved2);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:61:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved3’ [-Wparentheses]
   61 |   void (*__gtk_reserved3);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:62:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved4’ [-Wparentheses]
   62 |   void (*__gtk_reserved4);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:63:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved5’ [-Wparentheses]
   63 |   void (*__gtk_reserved5);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:64:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved6’ [-Wparentheses]
   64 |   void (*__gtk_reserved6);
      |        ^
/usr/include/gtk-2.0/gtk/gtkfilechooserbutton.h:65:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved7’ [-Wparentheses]
   65 |   void (*__gtk_reserved7);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:173,
                 from cc-interface.hh:26,
                 from cc-interface-png.cc:27:
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:76:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   76 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:77:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   77 |   void (*__gtk_reserved2);
      |        ^
In file included from /usr/include/gtk-2.0/gtk/gtk.h:173,
                 from graphics-info-modelling.cc:45:
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:76:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
   76 |   void (*__gtk_reserved1);
      |        ^
/usr/include/gtk-2.0/gtk/gtkstatusicon.h:77:8: 警告：unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
   77 |   void (*__gtk_reserved2);
      |        ^
graphics-info-modelling.cc: 在成员函数‘coot::rotamer_probability_info_t graphics_info_t::get_rotamer_probability(mmdb::Residue*, const string&, mmdb::Manager*, float, short int)’中:
graphics-info-modelling.cc:3636:33: 警告：catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
 3636 |       catch (std::runtime_error e) {
      |                                 ^
graphics-info-modelling.cc: 在成员函数‘short int graphics_info_t::update_residue_by_chi_change(int, mmdb::Residue*, atom_selection_container_t&, int, double)’中:
graphics-info-modelling.cc:3773:32: 警告：catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
 3773 |      catch (std::runtime_error rte) {
      |                                ^~~
graphics-info-modelling.cc:3778:33: 警告：catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
 3778 |       catch (std::runtime_error rte) {
      |                                 ^~~
make[1]: *** [Makefile:1445：cc-interface-png.o] 错误 1
make[1]: *** 正在等待未完成的任务....
mv -f .deps/globularize.Tpo .deps/globularize.Po
mv -f .deps/graphics-info-defines.Tpo .deps/graphics-info-defines.Po
mv -f .deps/globjects.Tpo .deps/globjects.Po
mv -f .deps/graphics-info-graphs.Tpo .deps/graphics-info-graphs.Po
mv -f .deps/graphics-info-gui.Tpo .deps/graphics-info-gui.Po
mv -f .deps/graphics-info-modelling.Tpo .deps/graphics-info-modelling.Po
mv -f .deps/graphics-info.Tpo .deps/graphics-info.Po
make[1]: 离开目录“/home/ywen232625/Downloads/coot-0.8.9.1/src”
make: *** [Makefile:590：all-recursive] 错误 1

Ramachandran HUD in rotamer selector?

Hi Paul,

When I use the rotamer selection interface, a HUD appears which I think shows the ramachandran plot (although in some kind of density format, no discrete residues shown). This plot is the same no matter which residue I center on, so it doesn't appear to be some kind of local metric. Is this a placeholder? Maybe a rotamer probability graph of some description would be useful here?

Cheers
Oli

gtk3 branch: warning: 'dialog_action_area1' is used uninitialized in this function [-Wuninitialized]

In the gtk3 branch, but not in master, an apparent error has been introduced into src/seq-view-interface.c. GCC diagnoses

In file included from /usr/include/glib-2.0/gobject/gobject.h:24,
                 from /usr/include/glib-2.0/gobject/gbinding.h:29,
                 from /usr/include/glib-2.0/glib-object.h:23,
                 from /usr/include/glib-2.0/gio/gioenums.h:28,
                 from /usr/include/glib-2.0/gio/giotypes.h:28,
                 from /usr/include/glib-2.0/gio/gio.h:26,
                 from /usr/include/gtk-3.0/gdk/gdkapplaunchcontext.h:28,
                 from /usr/include/gtk-3.0/gdk/gdk.h:32,
                 from /usr/include/gtk-3.0/gtk/gtk.h:30,
                 from seq-view-interface.c:21:
seq-view-interface.c: In function 'create_sequence_view_dialog':
/usr/include/glib-2.0/gobject/gtype.h:2224:12: warning: 'dialog_action_area1' is used uninitialized in this function [-Wuninitialized]
     ((ct*) g_type_check_instance_cast ((GTypeInstance*) ip, gt))
            ^~~~~~~~~~~~~~~~~~~~~~~~~~
seq-view-interface.c:58:14: note: 'dialog_action_area1' was declared here
   GtkWidget *dialog_action_area1;
              ^~~~~~~~~~~~~~~~~~~

GCC is quite right: the dialog_action_area1 pointer is declared in the function but never assigned a value (code that would make such an assignment has been commented out), and the uninitialized pointer is used unconditionally in a call to gtk_box_pack_start().

The function now contains code to emit a message "create_sequence_view_dialog(): dialog action area code removed", so perhaps that removal was incomplete?

clipper update related to reading ccp4 maps in mode 0

@pemsley et al:
we made a small change in clipper today, after consulting Kevin:
http://fg.oisin.rc-harwell.ac.uk/scm/loggerhead/clipper/trunk/revision/340
Please consider updating.
(I'm experimenting with mode 0 maps because the files are 4x smaller)

regression of rama Plot scoring between versio 0.941 and 0.95

Dear Paul,
We found that with version 0.95 of coot the Rama Plot scoring in the Accept refinement dialog of the real space refinement does not work properly any more. Although the refined part of the structure has no ramachandran outlier the panel shows that something is wrong (red indicator). With version 0.941 the very same part of the protein is indicated as OK in the dialog.
I have tested with the CCP4 and the standalone version. Both show the same behaviour.

Best wishes,
Christian

Suggestion: Homebrew formula for gtk3 (now GTK4) installation on macOS (or Linux)

Dear Paul,

I am a researcher in the field of bioinformatics, specifically structural biology.
I'm interested in the Coot software and want to use it. For my own interest and for the convenience of other macOS users, I have created a Homebrew formula to install Coot-gtk3 from the source code by referring to build-3-3 autobuild script in the gtk3 branch.

To start the installation of Coot-Gtk3 on a macOS with Homebrew, run the following command on the terminal app:

# install homebrew
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Install the latest coot (since Jul 17, 2024)
brew install brewsci/bio/coot

July 17, 2024, Now Coot can be installed from brewsci/homebrew-bio!

(May 14, 2024, Update the installation command. I provide coot bottles for macOS sonoma and Linux users)

(May 9, 2023, Update: Coot gtk3 now requires gtk 3.24.34, not the latest version. To use and pin it, see #33 (comment))

I would like to thank @wgscott and @keitaroyam for their support in creating this Formula. I would like to complete this Homebrew Formula for Coot so that Coot users can easily get access to the latest functions.

Refining/rotamer selection with two residues sharing alternative location?

I have a PDB file where I built two residues with alternative locations:

ATOM    939  N  AGLU E 199      33.272  31.560  33.627  0.50 48.23           N
ATOM    940  CA AGLU E 199      31.862  31.570  34.004  0.50 51.70           C
ATOM    941  C  AGLU E 199      31.478  30.325  34.793  0.50 53.08           C
ATOM    942  O  AGLU E 199      30.501  30.348  35.552  0.50 54.33           O
ATOM    943  CB AGLU E 199      30.983  31.710  32.762  0.50 54.36           C
ATOM    944  CG AGLU E 199      30.991  33.098  32.143  0.50 58.52           C
ATOM    945  CD AGLU E 199      30.216  33.153  30.844  0.50 70.32           C
ATOM    946  OE1AGLU E 199      29.620  32.121  30.472  0.50 79.24           O
ATOM    947  OE2AGLU E 199      30.202  34.219  30.191  0.50 65.14           O
ATOM    948  N  BLYS E 199      33.272  31.568  33.624  0.50 48.22           N
ATOM    949  CA BLYS E 199      31.860  31.572  33.998  0.50 51.73           C
ATOM    950  C  BLYS E 199      31.480  30.328  34.793  0.50 53.08           C
ATOM    951  O  BLYS E 199      30.511  30.355  35.561  0.50 54.30           O
ATOM    952  CB BLYS E 199      30.984  31.689  32.750  0.50 54.33           C
ATOM    953  CG BLYS E 199      30.965  33.079  32.120  0.50 58.59           C
ATOM    954  CD BLYS E 199      30.195  33.075  30.806  0.50 70.40           C
ATOM    955  CE BLYS E 199      30.262  34.425  30.102  0.50 66.17           C
ATOM    956  NZ BLYS E 199      29.581  34.401  28.771  0.50 61.53           N

This is a crystal structure of a protein with a mutation where both residues are present at this position in the structure. This should be a valid, see "Site shared by several chemical moieties" under "typical occupancy refinement scenarios and available options in phenix.refine" here ( http://www.phenix-online.org/newsletter/CCN_2015_07.pdf ) or PDB 1EJG ( https://www.rcsb.org/structure/1EJG ).

Phenix has no issues with refinement, but Coot/Wincoot does not cooperate at all (even with allow_duplicate_sequence_numbers() set). I can pick rotamers for the BLYS, but when I hit "OK" it fails:

Click on an atom in a residue for which you wish to see rotamers
setup_rotamers (1)
(0) " NZ ,B"/1/chainid="E"/199/LYS,  occ: 0.5 with B-factor: 61.53 element: " N" at (29.581,34.401,28.771) : 0.261882
setup_rotamers (0)
INFO:: backup file C:\WinCoot0893_7909\coot-backup/structure.pdb_Sat_Aug_10_10_18_39_2019_modification_1.pdb.gz
WARNING:: full_atom_spec_to_atom_index() Could not find " N  ","B"/199/E in this molecule: (0) C:\Users\user\Documents\Xtal\structure.pdb
DEBUG:: idx: -1
ERROR:: failed to find atom in molecule: chain-id :E: res_no 199 inscode :: name : N  : altloc :B:
ERROR:: bad atom index in replace_coords replacing atom: 1/E/199 {LYS}/ N   altLoc :B: segid :: pos: (33.272,31.568,33.624) B-factor: 48.22
WARNING:: full_atom_spec_to_atom_index() Could not find " CA ","B"/199/E in this molecule: (0) C:\Users\user\Documents\Xtal\structure.pdb
DEBUG:: idx: -1
ERROR:: failed to find atom in molecule: chain-id :E: res_no 199 inscode :: name : CA : altloc :B:
ERROR:: bad atom index in replace_coords replacing atom: 1/E/199 {LYS}/ CA  altLoc :B: segid :: pos: (31.86,31.572,33.998) B-factor: 51.73
WARNING:: full_atom_spec_to_atom_index() Could not find " C  ","B"/199/E in this molecule: (0) C:\Users\user\Documents\Xtal\structure.pdb
DEBUG:: idx: -1
ERROR:: failed to find atom in molecule: chain-id :E: res_no 199 inscode :: name : C  : altloc :B:
ERROR:: bad atom index in replace_coords replacing atom: 1/E/199 {LYS}/ C   altLoc :B: segid :: pos: (31.48,30.328,34.793) B-factor: 53.08
WARNING:: full_atom_spec_to_atom_index() Could not find " O  ","B"/199/E in this molecule: (0) C:\Users\user\Documents\Xtal\structure.pdb
DEBUG:: idx: -1
ERROR:: failed to find atom in molecule: chain-id :E: res_no 199 inscode :: name : O  : altloc :B:
ERROR:: bad atom index in replace_coords replacing atom: 1/E/199 {LYS}/ O   altLoc :B: segid :: pos: (30.511,30.355,35.561) B-factor: 54.3
WARNING:: full_atom_spec_to_atom_index() Could not find " CB ","B"/199/E in this molecule: (0) C:\Users\user\Documents\Xtal\structure.pdb
DEBUG:: idx: -1
ERROR:: failed to find atom in molecule: chain-id :E: res_no 199 inscode :: name : CB : altloc :B:
ERROR:: bad atom index in replace_coords replacing atom: 1/E/199 {LYS}/ CB  altLoc :B: segid :: pos: (30.984,31.689,32.75) B-factor: 54.33
WARNING:: full_atom_spec_to_atom_index() Could not find " CG ","B"/199/E in this molecule: (0) C:\Users\user\Documents\Xtal\structure.pdb
DEBUG:: idx: -1
ERROR:: failed to find atom in molecule: chain-id :E: res_no 199 inscode :: name : CG : altloc :B:
ERROR:: bad atom index in replace_coords replacing atom: 1/E/199 {LYS}/ CG  altLoc :B: segid :: pos: (31.1328,33.0073,31.9955) B-factor: 58.59
WARNING:: full_atom_spec_to_atom_index() Could not find " CD ","B"/199/E in this molecule: (0) C:\Users\user\Documents\Xtal\structure.pdb
DEBUG:: idx: -1
ERROR:: failed to find atom in molecule: chain-id :E: res_no 199 inscode :: name : CD : altloc :B:
ERROR:: bad atom index in replace_coords replacing atom: 1/E/199 {LYS}/ CD  altLoc :B: segid :: pos: (30.2293,33.0427,30.77) B-factor: 70.4
WARNING:: full_atom_spec_to_atom_index() Could not find " CE ","B"/199/E in this molecule: (0) C:\Users\user\Documents\Xtal\structure.pdb
DEBUG:: idx: -1
ERROR:: failed to find atom in molecule: chain-id :E: res_no 199 inscode :: name : CE : altloc :B:
ERROR:: bad atom index in replace_coords replacing atom: 1/E/199 {LYS}/ CE  altLoc :B: segid :: pos: (30.3983,34.3315,29.9743) B-factor: 66.17
WARNING:: full_atom_spec_to_atom_index() Could not find " NZ ","B"/199/E in this molecule: (0) C:\Users\user\Documents\Xtal\structure.pdb
DEBUG:: idx: -1
ERROR:: failed to find atom in molecule: chain-id :E: res_no 199 inscode :: name : NZ : altloc :B:
ERROR:: bad atom index in replace_coords replacing atom: 1/E/199 {LYS}/ NZ  altLoc :B: segid :: pos: (30.0017,35.5376,30.7642) B-factor: 61.53
INFO:: replace_coords: 0 atoms updated.
Model atom pick failed.

Sphere Refine+ doesn't even "see" the BLYS, and if I try to do a "Real Space Refine Zone", Wincoot crashes:

calling update_refinement_atoms()
gsl: ../gsl/gsl_vector_double.h:180: ERROR: index out of range
Default GSL error handler invoked.

[Edit] Adding allow_duplicate_sequence_numbers() fixes the crash on "Real Space Refine Zone", but still doesn't allow any refinement or rotamer selection of BLYS.

problem compiling coot_wrap_python.cc

I have made it far along the build process, with the 1.0.0 release code and I'm seeing this error now (I'm on a Rocky Linux 8.5/RHEL 8 clone):

libtool: compile: g++ -DPACKAGE_NAME="coot" -DPACKAGE_TARNAME="coot" -DPACKAGE_VERSION="1" "-DPACKAGE_STRING="coot 1"" -DPACKAGE_BUGREPORT="" -DPACKAGE_URL="" -DPACKAGE="coot" -DVERSION="1" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=".libs/" -DHAVE_OPENMP=1 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_PYTHON="3.9" "-DHAVE_BOOST=//" "-DHAVE_BOOST_PYTHON=//" -I. -DUSE_PYTHON -I.. -I/usr/include -DHAVE_SYS_STDTYPES_H=0 -I/root/glm/include -DCOOT_USE_GTK2_INTERFACE -I/usr/include/goocanvas-2.0 -I/usr/include/gtk-3.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/uuid -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/atk-1.0 -I/usr/include/at-spi2-atk/2.0 -I/usr/include/at-spi-2.0 -I/usr/include/dbus-1.0 -I/usr/lib64/dbus-1.0/include -pthread -I/usr/include/gtk-3.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/uuid -I/usr/include/harfbuzz -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/atk-1.0 -I/usr/include/at-spi2-atk/2.0 -I/usr/include/at-spi-2.0 -I/usr/include/dbus-1.0 -I/usr/lib64/dbus-1.0/include -pthread -I/panfs/hisoftware/cryoem/ssm/1.4/include -I/panfs/hisoftware/cryoem/mmdb2/2.0.22/include -DHAVE_SSMLIB -I/panfs/hisoftware/cryoem/mmdb2/2.0.22/include -DMMDB_HAS_LINK_DISTANCE -I/atavium/hisoftware/general/gsl/2.6/include -I/panfs/hisoftware/cryoem/clipper/2.1/include -I/panfs/hisoftware/cryoem/ccp4/6.5.1/include -I/panfs/hisoftware/cryoem/mmdb2/2.0.22/include -DCLIPPER_HAS_TOP8000 -I/panfs/hisoftware/cryoem/clipper/2.1/include -I/panfs/hisoftware/cryoem/fftw/v2.1.5/include -I/panfs/hisoftware/cryoem/ssm/1.4/include -I/panfs/hisoftware/cryoem/mmdb2/2.0.22/include -I/usr/local/lib64/python3.9/site-packages/PyGObject-3.36.1-py3.9-linux-x86_64.egg/include -DPKGDATADIR="/usr/local/share/coot" -DPACKAGE_LOCALE_DIR="/usr/local/share/coot/locale" -DPKGPYTHONDIR="/usr/local/lib/python3.9/site-packages/coot" -DPYTHONDIR="/usr/local/lib/python3.9/site-packages" -DDATADIR="/usr/local/share" -DCOOT_SYS_BUILD_TYPE="Linux-x86_64-\s-\sgtk3" -DCOOT_BUILD_INFO_STRING="" -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0 -I/root/python-3.8/lib/python3.8/site-packages/PyGObject-3.36.1-py3.8-macosx-11.5-x86_64.egg/include -I/usr/include/python3.9 -DHAVE_GSL -fopenmp -g -O2 -Wall -Wno-unused -std=c++11 -MT coot_wrap_python.lo -MD -MP -MF .deps/coot_wrap_python.Tpo -c coot_wrap_python.cc -fPIC -DPIC -o .libs/coot_wrap_python.o
In file included from /usr/include/gtk-3.0/gtk/gtk.h:100,
from globjects.h:30,
from coot_wrap_python.cc:2895:
/usr/include/gtk-3.0/gtk/gtkfilechooserbutton.h:66:8: warning: unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
void (__gtk_reserved1);
^
/usr/include/gtk-3.0/gtk/gtkfilechooserbutton.h:67:8: warning: unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
void (__gtk_reserved2);
^
/usr/include/gtk-3.0/gtk/gtkfilechooserbutton.h:68:8: warning: unnecessary parentheses in declaration of ‘__gtk_reserved3’ [-Wparentheses]
void (__gtk_reserved3);
^
/usr/include/gtk-3.0/gtk/gtkfilechooserbutton.h:69:8: warning: unnecessary parentheses in declaration of ‘__gtk_reserved4’ [-Wparentheses]
void (__gtk_reserved4);
^
In file included from /usr/include/gtk-3.0/gtk/gtk.h:271,
from globjects.h:30,
from coot_wrap_python.cc:2895:
/usr/include/gtk-3.0/gtk/deprecated/gtkstatusicon.h:74:8: warning: unnecessary parentheses in declaration of ‘__gtk_reserved1’ [-Wparentheses]
void (__gtk_reserved1);
^
/usr/include/gtk-3.0/gtk/deprecated/gtkstatusicon.h:75:8: warning: unnecessary parentheses in declaration of ‘__gtk_reserved2’ [-Wparentheses]
void (__gtk_reserved2);
^
/usr/include/gtk-3.0/gtk/deprecated/gtkstatusicon.h:76:8: warning: unnecessary parentheses in declaration of ‘__gtk_reserved3’ [-Wparentheses]
void (__gtk_reserved3);
^
/usr/include/gtk-3.0/gtk/deprecated/gtkstatusicon.h:77:8: warning: unnecessary parentheses in declaration of ‘__gtk_reserved4’ [-Wparentheses]
void (__gtk_reserved4);
^
coot_wrap_python.cc: In function ‘PyObject* _wrap_add_molecular_representation_py(PyObject*, PyObject*)’:
coot_wrap_python.cc:51877:17: error: ‘add_molecular_representation_py’ was not declared in this scope
result = (int)add_molecular_representation_py(arg1,arg2,arg3,arg4);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
coot_wrap_python.cc:51877:17: note: suggested alternative: ‘_wrap_add_molecular_representation_py’
result = (int)add_molecular_representation_py(arg1,arg2,arg3,arg4);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_wrap_add_molecular_representation_py
coot_wrap_python.cc: In function ‘PyObject* _wrap_remove_molecular_representation(PyObject*, PyObject*)’:
coot_wrap_python.cc:51906:3: error: ‘remove_molecular_representation’ was not declared in this scope
remove_molecular_representation(arg1,arg2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
coot_wrap_python.cc:51906:3: note: suggested alternative: ‘_wrap_remove_molecular_representation’
remove_molecular_representation(arg1,arg2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_wrap_remove_molecular_representation
make: *** [Makefile:2253: coot_wrap_python.lo] Error 1

It seems like there is just a missing header file from the source code. I don't even see this file in the latest version of the gtk3 branch -- not sure if its not autogenerated but there seems to be an issue with it.

Jeff

Build-it-3-3 also fails on a fresh installation of fedora 36

After doing...

wget https://raw.githubusercontent.com/pemsley/coot/gtk3/build-it-3-3
sudo dnf install g++ patch cmake python3-pip guile-devel
bash build-it-3-3

it fails with ls: cannot access '/home/murph/autobuild/Linux-fedora-gtk3/lib/python3.9/site-packages/numpy-*/numpy/lib/_version.py': No such file or directory ...

/home/murph/autobuild/Linux-fedora-gtk3/lib/python3.9/site-packages exists with a README.txt file only...

Thanks

missing header <string>

When building with a recent gcc version, I get this error

_BUILD_TYPE='"Linux-i686-debian-gnu/linux-gtk2"' -DCOOT_BUILD_INFO_STRING='""' 
-DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0      -DHAVE_GSL -fopenmp -g -O2 -MT 
c-interface-mogul.o -MD -MP -MF .deps/c-interface-mogul.Tpo -c -o 
c-interface-mogul.o c-interface-mogul.cc
c-interface-mogul.cc: In function ‘GtkCellRenderer* 
coot::mogul_results_add_cell_renderer(GtkTreeView*, GtkTreeStore*, const 
string&, int, int)’:
c-interface-mogul.cc:195:34: error: ‘strcpy’ was not declared in this scope

Original issue reported on code.google.com by [email protected] on 8 Jun 2013 at 9:38

refmac5 failed

Hi,

When I run a tutorial following "Coot Cryo-EM Tutorial 2: Fitting and Mutating", I met the error with warning info:"refmac5 failed". It happened when I started "Multi-sharpen using Refmac" from the Cryo-EM modules. Here is the specific error messages.
usage: refmac_window.py [-h] [--args Arguments] [--args_string Arguments]
[--job_location JOB_LOCATION] [--job_id JOB_ID]
[--project_location PROJECT_LOCATION] [--gui]
[--no-gui]
refmac_window.py: error: unrecognized arguments: MAPIN EMD-3908/map/emd_3908.map
(info-dialog "WARNING:: refmac5 failed")

Do you have any idea what is going on and how to fix it? Thank you.

Regards,
Bing

coot cannot open 3nir pdb

No idea what's the problem here, but I checked that ccp4MG opens this file without any problems.
In coot I get:

(get-ebi-pdb "3nir")
DEBUG:: in get-url-str: "3nir" "http://www.ebi.ac.uk/pdbe-srv/view/files/3nir.ent" pdb
INFO:: Creating directory coot-download
(handle-read-draw-molecule-with-recentre "coot-download/3nir.pdb.ent" 1)
INFO:: Reading coordinate file: coot-download/3nir.pdb.ent
WARNING:: Error reading small-molecule cif "coot-download/3nir.pdb.ent"
There was an error reading coot-download/3nir.pdb.ent. 
ERROR 42 READ: Duplicate sequence number and insertion code.
         LINE #1054
     ATOM    435  N  BSER A  22      -3.018 -12.669   4.880  0.36  2.28           N  

Spacegroup: P 1 21 1
There was a coordinates read error

a few automake/autoconf deprecated

Hello, when I run autogen.sh, I get this messages.
it would be nice to fix these old deprecated constructions

Cheers

Frederic

picca@mordor:~/Projets/coot$ ./autogen.sh 
libtoolize --copy --no-warn
aclocal -I macros
aclocal: warning: autoconf input should be named 'configure.ac', not 
'configure.in'
autoconf
automake --add-missing --copy
automake: warning: autoconf input should be named 'configure.ac', not 
'configure.in'
configure.in:31: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are 
deprecated.  For more info, see:
configure.in:31: 
http://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_
005fAUTOMAKE-invocation
automake: warning: autoconf input should be named 'configure.ac', not 
'configure.in'
analysis/Makefile.am:8: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
angles/Makefile.am:9: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
auxil/catcheck/Makefile.am:4: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/rama/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
auxil/sec-str/Makefile.am:3: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/strand-analysis/Makefile.am:5: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
auxil/vectors/Makefile.am:3: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
build/Makefile.am:25: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
ccp4mg-utils/Makefile.am:27: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
coords/Makefile.am:27: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
coot-surface/Makefile.am:21: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
coot-utils/Makefile.am:36: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
cootaneer/Makefile.am:23: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
cootilus/Makefile.am:23: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
db-main/Makefile.am:8: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
density-contour/Makefile.am:23: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
geometry/Makefile.am:27: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
goograph/Makefile.am:22: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
high-res/Makefile.am:29: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
ideal/Makefile.am:32: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
lbg/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
libgtkgraph/Makefile.am:2: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
lidia-core/Makefile.am:27: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
ligand/Makefile.am:26: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
mini-mol/Makefile.am:25: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
protein_db/Makefile.am:22: warning: 'INCLUDES' is the old name for 
'AM_CPPFLAGS' (or '*_CPPFLAGS')
skeleton/Makefile.am:24: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
src/Makefile.am:183: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
surface/Makefile.am:2: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' 
(or '*_CPPFLAGS')
tw/Makefile.am:28: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')
utils/Makefile.am:21: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or 
'*_CPPFLAGS')

Original issue reported on code.google.com by [email protected] on 8 Jun 2013 at 7:38

Main window will not shrink when toolbar is docked

If the toolbar is docked, issuing the set_graphics_window_size() command in the 
scripting window will not shrink the window beyond the toolbar size if the 
toolbar is docked.

I discovered this problem on my netbook, where the toolbar is actually longer 
than the screen height. Consequently, the --small-screen switch has no effect 
on the height of the window, which poses a problem.

If I undock the toolbar, the resize works as expected (except you can't shrink 
the window in the horizontal direction to be smaller than the menu.) 

One possible solution to this would be to select a set of smaller icons for the 
toolbar if the program discovers that it won't fit on the screen. The Mac OSX 
Gui can deal with the situation where the window becomes smaller than the menu. 
Perhaps there is a similar thing in GTK2.

I am running:
0.7-pre-1 (revision 3355)  [with python 2.6.5 embedded]
Binary type: Linux-x86_64-ubuntu-10.04.2-python-gtk2

Original issue reported on code.google.com by [email protected] on 7 Feb 2011 at 10:52

build-it-3-3 Error on New Ubuntu System

On new Ubuntu OS system (tried 18.04 / 22.04 ), the build-it-3-3 file always ends up with an error for coot build failed

BUILDING coot
coot build failed, exiting.

Is there a document that I can follow to install the same? The below link has very limited information
https://github.com/pemsley/coot/blob/master/INSTALL

autobuilding failed

Hi Paul,

I downloaded the coot-0.9.2 and try to install it on ubuntu follow the suggestion from the INSTALL file, that is to use the auto-builder. I guess there are some problems between the scripts and website because the scripts cannot download the correct package of the coot. Could you give me some advice to figure out it after you look through the output of the auto-builder.

Thank you very much.
###########
--2020-11-13 10:47:35-- http://skuld.bmsc.washington.edu/raster3d/Raster3D_3.0-3.tar.gz
Resolving skuld.bmsc.washington.edu (skuld.bmsc.washington.edu)... 128.95.235.53
Connecting to skuld.bmsc.washington.edu (skuld.bmsc.washington.edu)|128.95.235.53|:80... connected.
HTTP request sent, awaiting response... 304 Not Modified
File ‘/home/uf/autobuild/building/sources/Raster3D_3.0-3.tar.gz’ not modified on server. Omitting download.

Makefile:7: Makefile.incl: Permission denied
make: *** No rule to make target 'Makefile.incl'. Stop.
URL transformed to HTTPS due to an HSTS policy
--2020-11-13 10:47:36-- https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/.tar.gz
Resolving www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100
Connecting to www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... connected.
HTTP request sent, awaiting response... 300 Multiple Choices
Length: 629 [text/html]
Saving to: ‘/home/uf/autobuild/building/sources/.tar.gz’

.tar.gz 100%[==============================================================================================>] 629 --.-KB/s in 0s

Last-modified header missing -- time-stamps turned off.
2020-11-13 10:47:36 (22,6 MB/s) - ‘/home/uf/autobuild/building/sources/.tar.gz’ saved [629/629]

gzip: /home/uf/autobuild/building/sources/.tar.gz: not in gzip format
tar: This does not look like a tar archive
tar: Exiting with failure status due to previous errors
###########

part attachment of the INSTALL file:

Building Automatically

I'd say that the easiest way to try to build coot is to use the
auto-builder:

https://raw.githubusercontent.com/pemsley/coot/master/build-it

Crashes on torsion angle changes

What steps will reproduce the problem?
1. When I try to change a torsion angle with the "Edit Backbone Torsions"
tool, coot crashes on clicking ok.

What version of the product are you using? On what operating system?
I'm using Coot version 0.6.2-pre-1 on ubuntu. I have seen the same on centos

Thank you,

Thomas Schalch

schalch(at)cshl.edu

Original issue reported on code.google.com by [email protected] on 9 Apr 2010 at 12:39

run buit-it failed

/usr/bin/ld: ungz.o: in function `ungz_':
/home/ywen232625/autobuild/building/ywen232625-manjaro_2019-08-07__T14_30_24/Raster3D_3.0-3/ungz.c:20: 警告：the use of `tempnam' is dangerous, better use `mkstemp'
URL transformed to HTTPS due to an HSTS policy
--2019-08-07 22:37:54--  https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/pre-releases/right.tar.gz
已载入 CA 证书“/etc/ssl/certs/ca-certificates.crt”
正在解析主机 www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)... 131.111.85.100
正在连接 www2.mrc-lmb.cam.ac.uk (www2.mrc-lmb.cam.ac.uk)|131.111.85.100|:443... 已连接。
已发出 HTTP 请求，正在等待回应... 404 Not Found
2019-08-07 22:37:55 错误 404：Not Found。

I am trying to build coot in Manjaro, and I got this error.
It seems that this file does not exist.

[gtk3] Compilation and linking broken against recent Python versions

Hi Paul,
I took your recent Lunchtime Byte session at CCP4-SW as an opportunity to have a look at the GTK3 branch of coot. Fabulous work! Building coot and its dependencies has been difficult on modern Linux distributions (I am maintaining build scripts for Archlinux) and this new branch just (almost) builds out of the box.

However I stumbled upon some errors related to the Python version. Archlinux is a rolling-release distribution and hence ships with Python 3.9. Building then just fails with this error:

make[1]: Entering directory '/home/alex/git/coot/src'
g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9.9-pre\" -DPACKAGE_STRING=\"coot\ 0.9.9-pre\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9.9-pre\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_CXX11=1 -DHAVE_CXX_THREAD=1 -DHAVE_BOOST=/\*\*/ -I.  -I..  -I/usr/include  -DHAVE_SYS_STDTYPES_H=0       -I/home/alex/glm/include -DCOOT_USE_GTK2_INTERFACE   -DHAVE_GOOCANVAS -I/usr/include/goocanvas-2.0 -I/usr/include/gtk-3.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/harfbuzz -I/usr/include/freetype2 -I/usr/include/libpng16 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/lzo -I/usr/include/pixman-1 -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/gio-unix-2.0 -I/usr/include/cloudproviders -I/usr/include/atk-1.0 -I/usr/include/at-spi2-atk/2.0 -I/usr/include/dbus-1.0 -I/usr/lib/dbus-1.0/include -I/usr/include/at-spi-2.0 -pthread   -I/usr/include/ssm  -DHAVE_SSMLIB -DMMDB_HAS_LINK_DISTANCE  -I/usr/include -DCLIPPER_HAS_TOP8000     -DUSE_SQLITE3    -DPKGDATADIR='"/usr/local/share/coot"' -DPACKAGE_LOCALE_DIR='"/usr/local/share/coot/locale"' -DPKGPYTHONDIR='"/usr/local/lib/python3.9/site-packages/coot"' -DPYTHONDIR='"/usr/local/lib/python3.9/site-packages"' -DDATADIR='"/usr/local/share"' -DCOOT_SYS_BUILD_TYPE='"Linux-x86_64-arch-linux-pythongtk3"' -DCOOT_BUILD_INFO_STRING='""' -DUSE_LIBCURL -DHAVE_SYS_STDTYPES_H=0     -DUSE_PYTHON -I/usr/include/python3.9 -I/usr/include/python3.9  -DHAVE_GSL -fopenmp -g -O2 -Wall -Wno-unused  -MT c-interface.o -MD -MP -MF .deps/c-interface.Tpo -c -o c-interface.o c-interface.cc
In file included from /usr/include/python3.9/pytime.h:6,
                 from /usr/include/python3.9/Python.h:85,
                 from c-interface.cc:31:
c-interface.cc: In function 'PyObject* symmetry_operators_py(int)':
/usr/include/python3.9/object.h:130:30: error: expected '(' before '_Py_IS_TYPE'
  130 | #define Py_IS_TYPE(ob, type) _Py_IS_TYPE(_PyObject_CAST_CONST(ob), type)
      |                              ^~~~~~~~~~~
/usr/include/python3.9/boolobject.h:12:25: note: in expansion of macro 'Py_IS_TYPE'
   12 | #define PyBool_Check(x) Py_IS_TYPE(x, &PyBool_Type)
      |                         ^~~~~~~~~~
c-interface.cc:6086:7: note: in expansion of macro 'PyBool_Check'
 6086 |    if PyBool_Check(o) {
      |       ^~~~~~~~~~~~
c-interface.cc: In function 'PyObject* symmetry_operators_to_xHM_py(PyObject*)':
/usr/include/python3.9/object.h:130:30: error: expected '(' before '_Py_IS_TYPE'
  130 | #define Py_IS_TYPE(ob, type) _Py_IS_TYPE(_PyObject_CAST_CONST(ob), type)
      |                              ^~~~~~~~~~~
/usr/include/python3.9/boolobject.h:12:25: note: in expansion of macro 'Py_IS_TYPE'
   12 | #define PyBool_Check(x) Py_IS_TYPE(x, &PyBool_Type)
      |                         ^~~~~~~~~~
c-interface.cc:6112:7: note: in expansion of macro 'PyBool_Check'
 6112 |    if PyBool_Check(o) {
      |       ^~~~~~~~~~~~
make[1]: *** [Makefile:2097: c-interface.o] Error 1
make[1]: Leaving directory '/home/alex/git/coot/src'
make: *** [Makefile:697: all-recursive] Error 1

In addition to that, the output of python-config --ldflags has changed since Python 3.8 and does no longer include the Python libraries themselves (-lpython3.x). This will break linking even if the above mentioned error is fixed. An easy workaround is to use python-config --ldflags --embed. In addition to readding -lpython3.x this will also add -lutils on GNU/Linux. Manually adding the latter in macros/with-python.m4 may then not be necessary any more ;)

Regards,

Alexander

2TAA entry strangly overlaps with it's symmetry images

I fetch PDB entry 2TAA, and do Draw > Cell and Symmetry > show symmetry atoms.
Then I get an overlap that doesn't look right:

Multiple missing headers

I'm attempting to build Coot 1 from the release tarball at https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.tar.gz. After implementing a temporary workaround for issue #41, the build fails later, on account of a missing header:

In file included from meshed-generic-display-object.hh:12,
                 from coot-render.hh:15,
                 from molecule-class-info.h:80,
                 from graphics-info.h:79,
                 from main.cc:91:
Mesh.hh:10:10: fatal error: g_triangle.hh: No such file or directory
 #include "g_triangle.hh"
          ^~~~~~~~~~~~~~~

I don't find a header by that name anywhere in the source package or in this repository, and Google doesn't recognize it as a name from any common package. Further investigation seems to indicate other missing headers, too: at least map_triangle.hh and lights-info.hh.

Missing map_colour1 menu item

Coot 1 (gtk3) emits this diagnostic at startup:

(coot-bin:3227599): Gtk-CRITICAL **: 16:18:14.728: gtk_menu_item_set_submenu: assertion 'GTK_IS_MENU_ITEM (menu_item)' failed

This comes from gtk-manual.cc:create_initial_color_submenu(), and the ultimate cause appears to be that the a6.glade GUI description included in the distribution does not contain a definition for the "map_colour1" menu item.

set_background_colour() not working in no-graphics mode

I'm using Coot in --no-graphics mode to generate screeshots (through Raster3D), as part of Dimple pipeline.
Trying to address ccp4/dimple#5 I tried calling set_background_colour() in a script, but apparently it's a no-op in no-graphics mode.

So could you enable changing of the background without graphical interface? For example, by moving these lines in set_background_colour() in src/c-interface.cc:

   g.background_colour[0] = red; 
   g.background_colour[1] = green; 
   g.background_colour[2] = blue;

outside of if (g.use_graphics_interface_flag) { ... }.

Coot vs WinCoot performance

Hello,

This is just a question out of curiosity.

I have a dual boot set up (Windows 10 and Linux Mint 17.3), and I installed Coot on both operating systems. (WinCoot and Ubuntu binary).

I noticed that WinCoot performed much better than Coot when rotating and such.

So, since hardware is equal, what do you think makes Coot on Linux so slow in comparison to WinCoot?

build-it-3-3 fails with CentOS 7.9

Hi,
As per issue #57 the script runs but exits with coot build failed, exiting. Looking at the build logs, particularly 30-coot.txt, there is a number of compilation errors, all similar, example:-

coot_wrap_guile.cc: In function ‘scm_unused_struct* wrap_vector_mtz_type_label_ref(SCM, SCM)’:
coot_wrap_guile.cc:3691:24: error: ‘scm_listify__GONE__REPLACE_WITH__scm_list_n’ was not declared in this scope
SCM_UNDEFINED));
^
coot_wrap_guile.cc: In function ‘scm_unused_struct* wrap_vector_mtz_type_label_setN_(SCM, SCM, SCM)’:
coot_wrap_guile.cc:3732:24: error: ‘scm_listify__GONE__REPLACE_WITH__scm_list_n’ was not declared in this scope
SCM_UNDEFINED));
^
make[1]: *** [coot_wrap_guile.lo] Error 1
make[1]: Leaving directory `/s/ems/s/coot/build-coot/src'
make: *** [all-recursive] Error 1
make failed.

This error is a little beyond my C++ knowledge, any idea's how I can get past this ? As far as I can see in 24-guile.txt, the guile 2.2.7 install was fine.
Many Thanks for any help.

Some validation items not working

Hi,

Using the latest homebrew build for Mac, some Validation menu items are not working. Rotamers and B-factor are working, but the Ramachandran plot, Validation outliers and Ramachandran outliers do not display. Looking in the console, there are some errors when I click on these items:

ERROR:: glade file /usr/local/Cellar/coot/HEAD-7fb49cd/share/coot/dynarama.glade not found
WARNING:: could not initialise ramachandran

Traceback (most recent call last):
  File "/usr/local/Cellar/[email protected]/3.9.12/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/extensions.py", line 121, in <lambda>
    lambda func: validation_outliers_func())
  File "/usr/local/Cellar/[email protected]/3.9.12/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/extensions.py", line 118, in validation_outliers_func
    find_baddies.validation_outliers_dialog(aa_imol, imol_map)
NameError: name 'find_baddies' is not defined
Traceback (most recent call last):
  File "/usr/local/Cellar/[email protected]/3.9.12/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/coot/extensions.py", line 124, in <lambda>
    lambda func: rama_outlier_gui())
NameError: name 'rama_outlier_gui' is not defined

current svn doesn not compile on Debian7

Hello, it seem sthat the current svn does not compile on my Debian7 system

I got this error.

/bin/bash ../libtool --tag=CXX   --mode=link g++ -DHAVE_GSL  
-DPKGDATADIR='"/usr/local/share/coot"' -g -O2   -o test-hole test-hole.o 
./libcoot-coord-utils.la ../utils/libcoot-utils.la  
libtool: link: g++ -DHAVE_GSL -DPKGDATADIR=\"/usr/local/share/coot\" -g -O2 -o 
.libs/test-hole test-hole.o  ./.libs/libcoot-coord-utils.so 
../utils/.libs/libcoot-utils.so
/usr/bin/ld: test-hole.o: undefined reference to symbol 
'_ZN4coot16protein_geometry13init_standardEv'
/usr/bin/ld: note: '_ZN4coot16protein_geometry13init_standardEv' is defined in 
DSO /home/picca/Projets/coot/geometry/.libs/libcoot-geometry.so.0 so try adding 
it to the linker command line
/home/picca/Projets/coot/geometry/.libs/libcoot-geometry.so.0: could not read 
symbols: Invalid operation
collect2: error: ld returned 1 exit status


cheers

Frederic

Original issue reported on code.google.com by [email protected] on 21 May 2013 at 10:08

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