Molecule.append and reordering serials about htmd

[stefdoerr]

I seriously doubt that. Check the append code. At the end I do:
self.serial = np.arange(1, self.numAtoms+1)
Serials are never preserved in Molecule and should not be assumed to stay the same.

[j3mdamas]

You are right... I need to understand why is my cartoon representation breaking then.

[stefdoerr]

Bond problems. Can you check if there are bonds in your Molecules? If they are, can you check if after appending they are still correct in Licorice mode? (ignore NewCartoon for the moment)

[j3mdamas]

The Licorice representation is fine. Yes, there is bond information in
Molecule.bonds

On Fri, Apr 22, 2016 at 11:09 AM, Stefan [email protected] wrote:

Bond problems. Can you check if there are bonds in your Molecules? If they
are, can you check if after appending they are still correct in Licorice
mode? (ignore NewCartoon for the moment)

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#22 (comment)

[stefdoerr]

Before appending both Molecules look fine in newcartoon and after appending not anymore?
VMD uses given bonds but also guesses bonds based on distances. Can you disable it's bond guessing in mol.view(guessBonds=False) and try again ?

[j3mdamas]

I can give you more detail. I was appending the OPM beads onto the PDB.
Before NewCartoon works, after appending it doesn't. guessBonds=False does
not change.

In fact, the pdb straight from OPM has problems in representing the
cartoon. I thought it was the serial numbering (the OPM beads intercalate
the serials of the protein) but you are right and they are renumbered in
the append. Now I am guessing it's the residue numbering? I am going to
check it.

On Fri, Apr 22, 2016 at 11:18 AM, Stefan [email protected] wrote:

Before appending both Molecules look fine in newcartoon and after
appending not anymore?
VMD uses given bonds but also guesses bonds based on distances. Can you
disable it's bond guessing in mol.view(guessBonds=False) and try again ?

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#22 (comment)

[j3mdamas]

No, resid makes no sense...

On Fri, Apr 22, 2016 at 11:30 AM, Joao Damas [email protected] wrote:

I can give you more detail. I was appending the OPM beads onto the PDB.
Before NewCartoon works, after appending it doesn't. guessBonds=False does
not change.

In fact, the pdb straight from OPM has problems in representing the
cartoon. I thought it was the serial numbering (the OPM beads intercalate
the serials of the protein) but you are right and they are renumbered in
the append. Now I am guessing it's the residue numbering? I am going to
check it.

On Fri, Apr 22, 2016 at 11:18 AM, Stefan [email protected] wrote:

Before appending both Molecules look fine in newcartoon and after
appending not anymore?
VMD uses given bonds but also guesses bonds based on distances. Can you
disable it's bond guessing in mol.view(guessBonds=False) and try again ?

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#22 (comment)

[stefdoerr]

Ah then it's normal, if the original PDB also does not show Cartoon correctly. This happens in many cases because the connectivity cannot be guessed correctly. After building the system you will have a psf or prmtop with the correct connectivity and then it will be fine. You need to get used to that and just use Licorice before building if NewCartoon fails.

[j3mdamas]

Nope, the original PDB shows it correctly. The OPM beads break it

On Fri, Apr 22, 2016 at 11:36 AM, Stefan [email protected] wrote:

Ah then it's normal, if the original PDB also does not show Cartoon
correctly. This happens in many cases because the connectivity cannot be
guessed correctly. After building the system you will have a psf or prmtop
with the correct connectivity and then it will be fine. You need to get
used to that and just use Licorice before building if NewCartoon fails.

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#22 (comment)

[j3mdamas]

Test an example from OPM: http://opm.phar.umich.edu/pdb/1uaz.pdb

vmd 1uaz.pdb
Show NewCartoon

Seems more like a VMD than an HTMD issue...

On Fri, Apr 22, 2016 at 11:37 AM, Joao Damas [email protected] wrote:

Nope, the original PDB shows it correctly. The OPM beads break it

On Fri, Apr 22, 2016 at 11:36 AM, Stefan [email protected] wrote:

Ah then it's normal, if the original PDB also does not show Cartoon
correctly. This happens in many cases because the connectivity cannot be
guessed correctly. After building the system you will have a psf or prmtop
with the correct connectivity and then it will be fine. You need to get
used to that and just use Licorice before building if NewCartoon fails.

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#22 (comment)

[stefdoerr]

It's definitely a VMD "issue". But it's not something that can be fixed without building the system. VMD needs bonds to show Cartoon. If you guess bonds it will fail because of the OPM beads confusing the guesser. If you don't guess bonds it will fail because you don't provide all the protein bonds. Only way is to provide all protein bonds but that requires usually building the system first.