Hi Ed, C7 is the correct name for the atom. Instead of commenting out the line you could swap the C7 and the CM and then Refmac would correct the atom name if it is wrong. This is of course very user friendly, but it also keeps users from using the correct atom names (similar to the nucleic acid naming problem). So I prefer causing an error message.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Ed Pozharski > Sent: Monday, February 11, 2013 15:07 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] refmac5 MMA bug > > On Mon, 2013-02-11 at 09:56 +0100, Robbie Joosten wrote: > > This is a 'compatability' option in Refmac that internally renames > > atoms. If you comment out 'MMA . C7 CM' in your > > mon_lib_list.cif file, the problem will disappear. > > > > Robbie, > > thanks a lot - this fixes it. > > Is this still considered a bug? From what I understand, the > data_comp_synonym_atom_list entry indicates that whenever MMA C7 > atom is encountered, it will be internally renamed to CM. However, the > $CCP4_LIB/data/monomers/m/MMA.cif should then refer to CM as well. But > that cif-file still uses C7. > > Maybe this gets fixed in ccp4 updates, which reminds me to get that set up at > last. > > Cheers, > > Ed. > > -- > After much deep and profound brain things inside my head, I have decided > to thank you for bringing peace to our home. > Julian, King of Lemurs
