Bugs item #3588937, was opened at 2012-11-21 06:20 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3588937&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Angel Herraez (aherraez) Assigned to: Bob Hanson (hansonr) Summary: hetero [128] is not seen as ligand Initial Comment: 2gvd.pdb has a ligand named [128] which is not selected as "ligand" by Jmol 13.0.8 It is selected as "nucleic" due to ? being a nucleotide analog --though rather different ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2012-11-21 09:41 Message: I like the idea of single-residue groups rendering in ball and stick. ---------------------------------------------------------------------- Comment By: Angel Herraez (aherraez) Date: 2012-11-21 09:28 Message: Yes, I was aware of the ligand redefintion --and I am happy with it, I think it's better. The issue is why this ligand should be recognized as nucleic. It is quite different from a nucleotide. I guess it has the proper atom IDs to fit into Jmol algorithm? I assume there is no solution for this. The problem was, using standard defualt rendering of a pdb, the ligand is invisible. Perhaps single-residue "proteins" and "nucleics" could be selected somehow and applied ball and stick instead of cartoon... Something similar to C-only proteins and P-only nucleics getting a specific treatment. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2012-11-21 09:08 Message: correct. The definition of "ligand" was changed in 12.2. From the documentation: (originally "hetero and not solvent"; changed to "!(protein,nucleic,water,UREA)" I think you just have to work with that. Nothing I can think of would be the perfect "ligand" definition. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3588937&group_id=23629 ------------------------------------------------------------------------------ Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
