[phenixbb] Exploded ligands and phenix...

[Ralf W. Grosse-Kunstleve]

Hi Ruben,

> 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
looks reasonable.

> The log file can be downloaded here:
> files.me.com/ruben.vandermeeren/9tuifv

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)?

Ralf