Your .eff file must be explicitly referencing the Ca that you removed. Since it doesn't exist, phenix stops. Search your .eff file for the string "name CA and chain A and resname CA and resseq 1" (maybe a geometry.edit) and remove the reference.
I think the CCP4 bylines specifically encourage discussion of software other than ccp4, and i think this should be the case even if a discussion list exists for that software. Not everyone doing crystallography wants to sign up for 10 different mailing lists and get bombarded by the sometimes voluminous mail (CCP4, phenix, pymol, coot, xplor, sharp, solve, PDBL, sci.techniques.xtallography, bionet.xtallography, bionet.molbio.proteins, bionet.structural-nmr, bionet.molec-model, bionet.software.x-plor ) On 11/26/2014 11:09 AM, Almudena Ponce Salvatierra wrote:
Thank you all very much for your replies. However I am sorry this "ad" was a typing mistake of mine while transcribing the message. I have signed up for the phenixbb mailing list. And I will look up at the restraints that may still be there for this atom that I removed. Thanks again, best wishes, ALmudena 2014-11-26 15:58 GMT+00:00 Pavel Afonine <pafon...@gmail.com <mailto:pafon...@gmail.com>>: Hi Almudena, I am refining my structure with Phenix refine and I get the following error message just before starting: "no atom selected, "name CA ad chain A and resname CA and resseq 1". this is due to atom selection syntax error that you provided: after CA must be and not ad . I knew how to fix it once but I think I have forgotten now. Anyway, the only difference between the output model that came from the previous Phenix refine run and this one (the input for the new run) is that I removed a Calcium ion (this used to be chain A). So, if there is no chain A anymore, why does this appear? I have no clue. Any suggestions that will enable the continuation of this refinement will be more than welcome. I would do refinement run afresh. Perhaps you have some settings specific to that atom that got carried our to the next refinement run.. It's difficult to guess without more information. Pavel P.S.: there is Phenix mailing list for Phenix-specific questions. -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
