Yingyao Zhou

Improve Bio.PDB.mmcifio MMCIFIO to preserve original PDB chain ID

5

### Setup Currently, when MMCIFIO saves a structure to .cif, it rename chain IDs into A,B,C ... This renaming causes issues with other packages, such as crashing the logic in...

Patch fix_partial_contigs when residue numbering in PDB has a gap

2

In rf/utils.py, around line 78, should the 3 lines be added, in case the residue numbering in the original PDB file has a gap? Thanks! ``` if L > 0:...

MPNN designed sequence not separated correctly with multiple targets and multiple binders

2

With a toy example, my contig string is 'A 20 E 10' with a modified pdb structure. The output sequence is: TTCCPSIRSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN/RRRNNDKPVDMLYPMVAMEMTLGSEFEVME In the above output, the two target sequences...

atom index in af.prep.prep_pdb

1

In the prep_pdb.py file, line 434 ``` im = ignore_missing[n] if isinstance(ignore_missing,list) else ignore_missing if im: r = batch["all_atom_mask"][:,0] == 1 #

template cif contains insertion code

1

## Expected Behavior I would like to reuse a template folder for multiple ColabFold runs. So I run ColabFold first on the following input sequence: `>seq EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTV:NWFDITNWLWYIK:VQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGDGDLGKPIGAFAHWGQGTLVTVSS` If finds many...

## Expected Behavior Skip mmseq2 search. ## Current Behavior In code around line 1364 in colabfold/batch.py, it seems even when use_templates is True, a3m_lines is not None (use custom MSA)...

Is it possible to preserve some locations on a query sequence and only use ProGen to generate the remaining positions (conditioned generation)? Thanks!

Is there a way to mimic qsub, where the submission routine finishes immediately after submission? We are working on a web app, where the web app will submit a task...

I know this package is not maintained, but just curious if you are still able to shed some light on the issue I encountered. I want to use py3dmol to...

Try "aa" and "demo", see the following warning message before the output: 2025-02-07 13:23:11.374956894 [W:onnxruntime:, execution_frame.cc:812 VerifyOutputSizes] Expected shape from model of {1,BatchSize,64} does not match actual shape of {481,1,64}...