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 you want to exclude the use of a text editor in addressing this problem, then you should reach out to other software. I am sure there are several possibilities. For example MAIN procedure for solvent generation checks for overlapping atoms including symmetry mates (default cutoff is 1.9A) and removes them. //www-bmb.ijs.si/ best regards, dusan On Nov 1, 2014, at 1:00 AM, CCP4BB automatic digest system <lists...@jiscmail.ac.uk> wrote: > Date: Fri, 31 Oct 2014 08:32:56 +0800 > From: luzuok <luzuo...@126.com> > Subject: Re: AW: [ccp4bb] water at the same exactly position > > 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 there are clash_guard parameter with nonbonded_distance_threshold > = 0.5 . > I think I may try to turn of the clash_guard parameter. > > > Best Regards! > Lu Zuokun > > > > -- > 卢作焜 > 南开大学新生物站A202 Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS "Jozef Stefan" e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com
