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>: > 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
