[Biopython-dev] Questions on StructureBuilder, MMCIFParser, and MMCIFlex

[Peter]

On Tue, Nov 3, 2009 at 4:36 PM, Paul B <tallpaulinjax at yahoo.com> wrote:
>
> Hi,
>
> I have found the reason why MMCIParser is dying. It has no provision
> for more than one model, so when a second model comes around with
> the same chain and residue the program throws an exception.

Please file a bug report on bugzilla for that. I guess no-one has tried
NMR CIF data with the parser before (!).

> I will be joining github to submit the required changes. I haven't used
> github before, and this is my first open source project so please give
> me a few days to acclimate.

I you like - great. Otherwise we can manage with patches via an
enhancement bug on bugzilla.

> My mods so far are as follows in MMCIFParser.py (and require the
> MMCIFlex.py and MMCIF2Dict.py files I will be submitting via github,
> and have submitted to Peter privately.)

Actually, I think that ended up on mailing list:
http://lists.open-bio.org/pipermail/biopython-dev/2009-November/006938.html

> The only difference is the PDBParser incorrectly states the first model as 0
> when it should be 1: there is an explicit MODEL line in pdb2beg.ent. So all
> the models are off by one in 2beg when parsed by PDBParser.py. I can
> look into the bug in PDBParser.py and submit it if desired?

Are you sure it should it be 1 and not 0? Remember, Python counts from zero.

Peter