Check other Cl- in the pdb to see whether the bond lengths and VdW are an issue (wouldn't H2O have the same VdW issues?). I am thinking (this happened to me once by mistake) that maybe you are using the last updated mtz (output of refinement) to refine against rather than the original one. This for some reason can put weird blobs of density in cavities, and confused me once. I am still somewhat curious why this happens, since I would think Refmac would just use obs amplitudes (maybe it's reading Fcalc rather than Fobs?)
JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carlos CONTRERAS-MARTEL Sent: Wednesday, January 21, 2015 9:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] chloride or water Hi Rohit, What about your Rfree? what about your protein geometry? I will try to figure out this residual density at the realy latest step of the refinement. Because of your resolution, no anomalous signal available and Van der Waals problems it could be difficult for a referee believe in a Cl ion. That you probably wants to describe like close to you active site, so of some relevance for the activity. All the best Carlos -- Carlos CONTRERAS MARTEL, Ph.D. (CR1 CNRS) carlos.contreras-mar...@ibs.fr "Bacterial Pathogenesis Group" Institut de Biologie Structurale UMR5075 CEA-CNRS-Université Joseph Fourier Grenoble 1 IBS 71, avenue des Martyrs CS 10090 38044 Grenoble CEDEX 9 FRANCE tel : (+33) (0)4 57 42 86 41 http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/ http://www.ibs.fr/groups/bacterial-pathogenesis-group/
