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I got the following error when trying to download BFD_1.3M.hdf5
at https://figshare.com/articles/dataset/Protein_structures_predicted_using_DMPfold2/14979990?file=28893897
{"message": "Storage exception: Unexpected scenario inst_id=549 state=ic_failure", "code": "StorageException”}

It seems the file is incompletely uploaded.

I noticed that input alignments with characters "X" and "N" cause a KeyError at line 202 of the predict.py script. Obviously DMPfold2 is only set up to handle the basic 20 amino acid alphabet.

Do you have any recommendations for how to generate predictions from such alignments without simply removing columns with ambiguous characters?

hey
I have an issue:
Traceback (most recent call last):
File "/home/marcin/anaconda3/envs/dmpfold2/bin/dmpfold", line 5, in
run_dmpfold()
File "/home/marcin/anaconda3/envs/dmpfold2/lib/python3.8/site-packages/dmpfold/predict.py", line 202, in run_dmpfold
atomnum, an, rnamedict[alnmat[0,ri]], ri + 1,
KeyError: 21

Do you know what could be wrong?

I use dmpfold2 on cpu
0: AMD Ryzen 9 3950X
Microarchitectures:
32x Zen 2
<32gb RAM

Hi, dmpfold is really fast! Thanks!
I would like to know if dmpfold has been further evaluated by building side-chain conformations to the output backbone structure?
If yes, which package do you recommend to build side-chain conformations after dmpfold?

Hey again
Another problem... I want to run dmpfold2 on other computer and get this:

(dmpfold) marcin@marcin-Precision-7920-Tower:/mnt/7fee140a-a85e-4bbb-96b1-4a34cdb806c1$ dmpfold -i PF10963.aln -d cuda:0 > fold.pdb
Traceback (most recent call last):
File "/home/marcin/anaconda3/envs/dmpfold/bin/dmpfold", line 5, in
run_dmpfold()
File "/home/marcin/anaconda3/envs/dmpfold/lib/python3.8/site-packages/dmpfold/predict.py", line 184, in run_dmpfold
coords, confs, alnmat = aln_to_coords(args.input_file, device=args.device,
File "/home/marcin/anaconda3/envs/dmpfold/lib/python3.8/site-packages/dmpfold/predict.py", line 128, in aln_to_coords
alnmat = (np.frombuffer(''.join(aln).translate(aa_trans).encode('latin-1'), dtype=np.uint8) - ord('A')).reshape(nseqs,length)
UnicodeEncodeError: 'latin-1' codec can't encode character '\u21b5' in position 102630: ordinal not in range(256)
(dmpfold) marcin@marcin-Precision-7920-Tower:/mnt/7fee140a-a85e-4bbb-96b1-4a34cdb806c1$

do you know what could be wrong?
all best
Marcin

Update
its my fault, bad input

Hi, I was trying to run DMPfold2, but the next error appeared:

Traceback (most recent call last):
File "./dmpfold", line 5, in
run_dmpfold()
File "/home/esgarle/.local/lib/python3.8/site-packages/dmpfold/predict.py", line 175, in run_dmpfold
coords, confs, alnmat = aln_to_coords(args.input_file, device=args.device,
File "/home/esgarle/.local/lib/python3.8/site-packages/dmpfold/predict.py", line 121, in aln_to_coords
alnmat = (np.frombuffer(''.join(aln).translate(aa_trans).encode('latin-1'), dtype=np.uint8) - ord('A')).reshape(nseqs,length)
ValueError: cannot reshape array of size 1977853 into shape (10740,41)

I am not sure if this error is related to the size of the input file, with aln format. It contains around 1500 sequences.

Is there any specification for .aln format available? Or are there any tools converting from .a3m format to .aln?

I did google for .aln specification, but nothing found. I had tried also using converter from https://github.com/soedinglab/hh-suite/blob/master/scripts/reformat.pl, but non of the output had matched provided example (https://github.com/psipred/DMPfold2/tree/master/dmpfold/example/PF10963.aln).

I did check also online version of HHblits, but also did not found way to download results in your format. Here is my job:
https://toolkit.tuebingen.mpg.de/jobs/8863800

Sequence I'm looking alignment for is MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVASAAGGNEPSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIP

My a3m file: rcsb_pdb_2GAF_part.a3m.txt