Dear colleagues, I have been iteratively rebuilding and refining a crystal structure using coot (v. 0.9.8.91) and Phenix.
Refinement makes use of NCS restraints, and the structure additionally has some covalent links between protein sidechains and bound ligands. NCS parameters and links are output by Phenix in both PDB and mmCIF file formats. Coot happily opens the PDB file, and the covalent links are displayed as the usual dotted lines. However, coot fails to open the mmCIF file. According to an old ccp4bb post (https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1910&L=CCP4BB&D=0&P=73942), this appears to be an mmdb2 library issue that I gather has not been resolved. In particular, the _struct_ncs_oper category in the mmCIF is the culprit and - as the previous poster noted - removing this whole section from the file enables coot to open it. I gather this is akin to deleting the MTRIX section in a PDB file, though am not sure whether this is either permitted or advisable for a deposited structure. Additionally, coot doesn’t show the sidechain-ligand links in this modified mmCIF file. The correct _struct_conn.id loops are present – is there a switch somewhere that encourages coot to show them? I’ve checked other deposited mmCIF files with such links, and they too suffer from the same problem. As I’m now depositing the structure at the PDB, I’m trying to resolve these issues prior to accepting the final annotated version. While end users will always be able to open the PDB file in coot, mmCIF seems to be the preferred file type for many. Apologies if I’ve missed other posts/solutions to these issues, or have misunderstood something – I did search, but could not find answers. Any suggestions would be extremely welcome! Since mmdb2 is managed by the CCP4 team, I will likely post this to ccp4bb also. With thanks in advance, Neil -- Neil Rzechorzek PhD Principal Laboratory Research Scientist DNA Recombination and Repair Lab (Stephen West) The Francis Crick Institute 1 Midland Road London NW1 1AT T: 020 3796 0601 E: [email protected]<mailto:[email protected]> W: www.crick.ac.uk The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
