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

[Paul B]

Hmmm... no matter whether there is a (explicit first parsed) MODEL record or not in the PDB file, PDBParser currently records the model id as 0. I can see that being the choice if there wasn't a MODEL record. But if there IS a MODEL record of 1, the model id should be forced to 0? What if the MODEL records exists, and for some reason it is MODEL 2 and that's the first record PDBParser parses? Should that also have a forced model id of 0? This seems to me to be a bug instead of a feature. I'd hate to promulgate that error in the MMCIFParser code as well. Someone could be thinking they are doing a study on model X when really they are studying X+1, or worse yet X+Y where Y is the offset between the forced 0 id and the true first model id. And if the models in the file has skips, ie, MODEL 1 then 3,4,7, and 9... those should be model id's 0 through 4? I don't know if that can happen, just saying... But if the TRUE model record information is not trapped
 (and it's not), how would someone know what true model they are looking at instead of the forced model id that starts at 0?
 
Not to rock the boat, but food for thought. I can make MMCIFParser match whatever is deemed to be the correct thing to do.
 
Paul
 
--- On Tue, 11/3/09, Peter <biopython at maubp.freeserve.co.uk> wrote:


From: Peter <biopython at maubp.freeserve.co.uk>
Subject: Re: [Biopython-dev] Questions on StructureBuilder, MMCIFParser, and MMCIFlex
To: "Paul B" <tallpaulinjax at yahoo.com>
Cc: "Biopython Development" <biopython-dev at biopython.org>
Date: Tuesday, November 3, 2009, 4:54 PM


On Tue, Nov 3, 2009 at 5:34 PM, Paul B <tallpaulinjax at yahoo.com> wrote:
>>Are you sure it should it be 1 and not 0? Remember, Python counts from zero.
>
> If the MODEL record in the .ent record says MODEL 1, should
> biopython report it as 0? In PDBParser, the code is as follows:
> ...

If for the PDB parser Thomas already chose to report the model
as 1, then to yes you are right - to be consistent the CIF parser
should do the same as the PDB parser.

Peter