[Biopython] The PDBParser Permissive setting

[João Rodrigues]

Hey Mark,

What kind of validation do you want?

Cheers,

João
No dia 17 de Jul de 2012 02:52, "Mark Livingstone" <
livingstonemark at gmail.com> escreveu:

> Hi Guys,
>
> In my code I am experimenting with different ways of doing RMSD
> calculations. I have code which in addition to normal CA based RMSD
> can do (CA & CB) RMSD and also sidechain RMSD. On a perfect PDB file
> this works well. Unfortunately, the curation I have is fairly average
> / poor in quality :-( and I only find out when one of the liberal
> number of Try/Except blocks falls over.
>
> I need a better way to find out sooner if a PDB file is missing data.
>
> I am wondering therefore is for PDBParser I set Permissive=0, and
> after setting the relevant models and chains etc, I did
>
>
> wt_atoms = Bio.PDB.Selection.unfold_entities(wtc, 'A')
>
> If this successfully works without throwing an Exception, can I assume
> that this unfolded chain is perfect, or are there ways that I could
> still be tripped up?
>
> Alternatively, can anyone suggest code that I can employ in my
> curation process that will give me a decent sanity check of PDB
> quality, so I can get on writing experimental code - and not
> Try/Except blocks :-(
>
> Thanks in advance,
>
> MarkL
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>