Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?

[Youval Dar]

Hi Tim,

While we did not make this information available yet, there is a way to get 
"non-bonded  clash score" that does take into account symmetry related clashes  
using the Phenix command:
>>> phenix.pdb_interpretation xxxx.pdb nonbonded_clashscore=True

Testing for clashes is done in a slightly different method than the one in 
MolProbity, so the clash score for clashes not due to symmetry will not be 
exactly the same as the clash score produced by MolProbity.

So for example running from the command prompt
>>> phenix.fetch_pdb 1d11
>>> phenix.pdb_interpretation 1d11.pdb nonbonded_clashscore=True

will produce a report ending with:

  Nonbonded clashscore
    Without symmetry operation and solvent-solvent clashes:   12.35
    Due to symmetry operation:                                               
32.92
    Solvent-solvent:                                                            
     8.23
    Total:                                                                      
           53.50


Thanks