[phenixbb] Clashes problem

Karolina Michalska dziuba at amu.edu.pl
Mon Feb 11 05:13:16 PST 2008

Basically I have the same observation. My structure looks good (1.7A,
R=19.6 free=22.5; strategy=individual_sites+individual_adp+tls; twin fr.
0.47) with nice geometry and density, but the clashscore in Molprobity
is terrible. Almost all residues form clashes. It is improved only
slightly if I add hydrogens at riding positions. So I am also curious
where the problem is...


Dnia 11-02-2008, pon o godzinie 13:02 +0000, Simon Kolstoe napisał(a):
> Dear Phenix community,
> I am using phenix.refine version 2007_08_18_1856 to refine a 2.65A  
> structure (with individual_sites, group_adp, TLS & NCS,  
> wxc_scale=0.1). After refinement I am running the pdb file through the  
> Molprobity server. Molprobity gives a clash score of 33.78 indicating  
> the number of steric clashes (within 0.4A) per 1000 atoms.
> I am slightly concerned that a refinement program seems happy to allow  
> such clashes. Is this a problem with the version of phenix.refine I am  
> running, or is there a more obvious explanation that I have missed?
> Thanks,
> Simon 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list