Re: [ccp4bb] refmac5 MMA bug
Hi Ed, 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. Cheers, Robbie Date: Sun, 10 Feb 2013 23:35:25 -0500 From: epozh...@umaryland.edu Subject: [ccp4bb] refmac5 MMA bug To: CCP4BB@JISCMAIL.AC.UK I see a strange issue with a model that includes O1-methyl-mannose (three letter code MMA). Basically, refmac fails and says that C7 is missing in the model while CM is absent from the library. The problem is that there is no CM atom in the pdb file, while C7 is right there. This happens with Refmac_5.7.0029, and I see no obvious issues with the corresponding cif-file in the monomer library. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
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
Re: [ccp4bb] refmac5 MMA bug
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
[ccp4bb] refmac5 MMA bug
I see a strange issue with a model that includes O1-methyl-mannose (three letter code MMA). Basically, refmac fails and says that C7 is missing in the model while CM is absent from the library. The problem is that there is no CM atom in the pdb file, while C7 is right there. This happens with Refmac_5.7.0029, and I see no obvious issues with the corresponding cif-file in the monomer library. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
