Dear Lou,
the simplest solution is to delete all waters from your PDB file by a text
editor and then insert them again with any automated procedure you have at hand.
You can also use validation programs which will provide you with this
information and then delete the overlapping solvents.
If
ould just
crash and do not have options to clean-up the waters before starting refinement.
Best regards,
Herman
Von: luzuok [mailto:luzuo...@126.com]
Gesendet: Freitag, 31. Oktober 2014 01:33
An: Schreuder, Herman R&D/DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re:[ccp4bb] AW: [ccp4bb] water at
Dear Herman,
If there are duplicate atoms in my PDB, Phenix refine GUI will post error
and crash (Sorry I haven't tried other refinement program). And there is no
.geo output file if program crash.
Phenix refine thought them as nonbonded atoms with distance equal to 0.
Because the
Dear Lu,
I don’t see your problem. Why don’t you use the automatic water update option,
present in most modern refinement programs, as Pavel suggested? This should
take care of your problem.
Of course, having premium, 1st class hand-picked waters is still the gold
standard, but I don’t believe
