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 scripts. 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 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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