[Biopython] The PDBParser Permissive setting

[Mark Livingstone]

Hi João,

I guess it would be good if I could get a data structure that had no
discontinuities, no missing data points or unknowns. I would be able
to tell it to ignore HOH or other irrelevancies.

My use case as I mentioned is RMSD and similar algorithms, so one
continuous structure with all the data attached that I can iterate
through, selecting atoms / residues as needed, and get the names and
coordinates as I go.

So I guess I want a PDB Diagnostic type program to allow me to find
exemplary PDB files to use during initial stages of development while
I do proof of concept, since I know that finding edge case PDBs for
later work is not as hard it seems as finding good ones ;-) Maybe the
simplest way to think of the sort of PDBs is you can run your software
and you don't need any try / except blocks for Biopython to work well
:-D

Cheers,

MarkL

On 17 July 2012 16:42, João Rodrigues <anaryin at gmail.com> wrote:
> 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
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