[phenixbb] Exploded ligands and phenix...
Ralf W. Grosse-Kunstleve
rwgk at cci.lbl.gov
Tue Apr 28 15:56:30 PDT 2009
> The cryst1 card of the pdb is the next:
> CRYST1 98.500 104.050 415.200 90.00 90.00 90.00 P 21 21 21
I tried phenix.pdbtools --geometry-regularization again after
adding this CRYST1 card. The result looks good, i.e. symmetry
interactions don't seem to be the problem.
> For non-bound interactions the distance is sometimes
> less than the VDW-radius. Could this be the problem?
No, I don't think so. Your histogram of nonbonded interaction distances
> The log file can be downloaded here:
Clearly, the .cif file is read, otherwise phenix.refine would stop
very early on.
Sorry, I still don't know what's going wrong. Could you send me the
phenix.refine inputs for debugging (to me directly, not to phenixbb)?
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