[phenixbb] Phenix.molprobity PDB pre-test

Oleg Sobolev osobolev at lbl.gov
Fri Feb 9 10:58:38 PST 2018

Hi Ruki,

I would suggest you to try phenix.pdb_interpretation - This will parse your
model and try to construct geometry restraints for it using Phenix
restraints library. In the process, many strange things are being diagnosed
and reported.
More lightweight and fast tool is phenix.pdb.hierarchy - this will only
parse model and construct internal representation of it that is used in
phenix. Some errors also could be detected here, but the amount of analysis
is much less compared to phenix.pdb_interpretation.

To gain even better control, you can use cctbx library (
https://github.com/cctbx/cctbx_project), which contains all the necessary
tools used by Phenix. Then you will be able to write your own Python

Let us know if you need more information on any Phenix tools.

Best regards,
Oleg Sobolev.

On Fri, Feb 9, 2018 at 12:12 AM, Rune Thomas Kidmose <rtk at mbg.au.dk> wrote:

> Hi,
> After using Phenix.molprobity I noticed it does a test of the input PDB
> file in the beginning, where it, among other things, identifies duplicate
> atom labels and then proceeds to list some of them (and hides the rest some
> where I guess).
> It also identifies mismatches between the atom label and the atom type,
> e.g. if a CB is by mistake listed as an O instead of a C, in the last
> column in the PDB file.
> I would like to know if it is possible to somehow call this PDB pre-test
> function used within phenix.molprobity? or maybe something similar in the
> phenix package?
> I would like to use the feature in a small MD pipeline I am developing
> where the input PDB files are checked for duplicate atoms and mismatches
> between atom label and type. I believe something like the mentioned
> pre-test feature would work much better, than my current bash script
> solutions using combinations of awk, grep, sort, uniq etc.
> Cheers
> Ruki
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