[BioPython] Bio.PDB : loading Big PDB with segments

[Arturas Ziemys]

Hi,

Whose PDB files are generated by NAMD or VMD. NAMD is molecular dynamics programs and VMD for structure manipulation and visualization. My modeled systems - and believe the systems of others in MD - are big in sense that these PDB files exceeds the limits in resid or serials. For example, as far I understant, unification of atoms in VMD is made with segment information and it has no problems with that. 

In my opininion those files follow PDB format. At least I found no differences in column structure or column content of PDB. It seems that Bio.PDB just takes the segment's identities as some record to ATOM entry, but they are meaningless making them unique or original if the records with the same serial are met in PDB. After I tryed to load those files, I got plenty errors and the "dublicated" entries were just skipped.

I could do some "preproccesing" on PDB supplying chain identifier foer each segment each time load PDB files and remove supplied chain labbels each time on exit. But I am interested is there any another way ?

I could attach as an examle, but comppressed file is ~ 1MB, uncompressed > 5 MB. If it is OK with the size - I can send a PDB file.

Arturas


>
>Arturas Ziemys wrote:
>> HI
>> 
>> I deal with big PDB files, but PDB files have different segments and
>> each segments have restarted residue id numbering, because each time
>> it exceeds 9999: when I load such a PDB file, I get error each time
>> the line with the same resid number from another segment is met. It
>> seems those lines are skipped and are not loaded.
>> 
>> Does anybody knows how to tune Bio.PDb module to correct it or any
>> other way ?
>
>Are these "big PDB files" downloaded directly from the PDB, another 
>database, or generated by some other software?
>
>If they are publicly available could you post a link so other people can 
>investigate a little more (e.g. example PDB ID codes)
>
>Do you know enough about the file format to say if these files are 
>following the standard or breaking it?  (If we do need to fix the parser 
>it has a permissive mode (default) and a strict mode).
>
>Peter
>