iochris / ahoj Goto Github PK

Fantastic tool, thank you! :)
Just a small suggestion for improvement: When running a query, a progress bar is shown for each download of the resulting files, each taking <1 s (making the progress bar somewhat useless). It would be more meaningful to have the progress bar indicate the overall progress (downloaded structures/total structures to be parsed).

When query sequence is longer than candidate sequence, TM align can be poor enough to discard the structure, even if they align well. In such cases, the candidate structures are discarded and not featured in the results, despite of their binding site(s) overlapping with the query. This is a recurring scenario when there is a size difference between query and candidate (long query seq - short candidate seq.).

query "1fmk A HOH 1011" misses hit candidate "4hxj" which should be there as it covers the binding site.
At the same time it picks up structures that do not cover the binding site.

Example:
python apoholo.py --query "2v57 a,c prl"
fails with
pymol.CmdException: Error: Malformed selection.

The message could contain a note that the chain names are case sensitive.