Menu
▾
▴
[Jmol-developers] [ jmol-Bugs-1014891 ] Backbone/trace limitation
|
From: SourceForge.net <no...@so...> - 2004-08-24 19:09:43
|
Bugs item #1014891, was opened at 2004-08-23 19:02 Message generated for change (Comment added) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1014891&group_id=23629 Category: Applet Group: None Status: Open Resolution: None Priority: 5 Submitted By: de Banzie (debanzie) Assigned to: Miguel (migueljmol) Summary: Backbone/trace limitation Initial Comment: Some pdb files limit protein data to alpha carbons (e.g., 1ffk) or nucleic acid data to phosphate groups (e.g., 1JGQ). The jmol applet does not appear to be able to generate a backbone or trace display with this data (unlike Chime). ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2004-08-24 12:09 Message: Logged In: NO I took a look at 1JGQ. I am confident that we can add some minimal support for Phosphorus-Only nucleotide chains. However, it will be *after* the official v10 release of Jmol. ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-08-24 12:00 Message: Logged In: YES user_id=1050060 I took a look at 1FFK ... that is a BIG file ... 64K atoms ... takes 83 seconds to read on a 3 year-old 1Ghz Celeron running Linux. Once it is loaded, backbone & trace all work fine. When running as an applet it is possible that there is a memory size issue. ---------------------------------------------------------------------- Comment By: Miguel (migueljmol) Date: 2004-08-23 19:24 Message: Logged In: YES user_id=1050060 Jmol should support alpha-carbon only pdb models. I will take a look at 1FFK later. There is currently no support for 'phosphate groups only' on nucleic acids. I am not a chemist. It would be very helpful to me if you could explain which atoms exist in a phosphate-only nucleic acid. Do they *all* look just like 1JGQ ? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1014891&group_id=23629 |