[Biopython] The PDBParser Permissive setting

[Mark Livingstone]

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