Re: [PyMOL] distance bug
Hi, My pymol 1.4.1 works fine. can you try to ray trace and see if your objects are available but just not displayed on the standard screen? cheers, 2011/9/29 Andreas Förster docandr...@gmail.com Hi all, Has anyone noticed that the distance command behaves oddly. Has this been recently introduced? fetch 1ubq zoom 1ubq dist 9/cg2, 73/cd2 # output: object dist01 is created # distance of 10.2 is shown, but no dashed line # now check this out: # several repetitions of the next two lines disable dist01 enable dist01 # eventually lead to the appearance of the dashed line # but it gets better disable dist01 enable dist01 # The distance is enabled but neither number nor dashed line are visible disable dist01 enable dist01 # Now the number and the dashed line are back When dist01 is enabled but invisible, disabling 1ubq brings it back, but it disappears again when 1ubq is re-enabled. With other pdb files, the distance command doesn't work at all. It returns a distance of 0.0A to the screen that is only visible when the associated pdb object is disabled. I've observed this with pymol-py26 1.4-7 installed with fink on a MacBook running 10.6 and with pymol 1.4.1 revision 3968 installed through svn on RHEL 6.1 Notably, earlier revisions (e.g. 3958 and 3945) on RHEL 6.1 work just fine. Recently introduced bug? Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] distance bug
Hi Andreas, It was a bug with the invalidation system. I just pushed a fix to source forge. Thanks for bringing this to our attention. Cheers, -- Jason 2011/9/29 Andreas Förster docandr...@gmail.com: Hi all, Has anyone noticed that the distance command behaves oddly. Has this been recently introduced? fetch 1ubq zoom 1ubq dist 9/cg2, 73/cd2 # output: object dist01 is created # distance of 10.2 is shown, but no dashed line # now check this out: # several repetitions of the next two lines disable dist01 enable dist01 # eventually lead to the appearance of the dashed line # but it gets better disable dist01 enable dist01 # The distance is enabled but neither number nor dashed line are visible disable dist01 enable dist01 # Now the number and the dashed line are back When dist01 is enabled but invisible, disabling 1ubq brings it back, but it disappears again when 1ubq is re-enabled. With other pdb files, the distance command doesn't work at all. It returns a distance of 0.0A to the screen that is only visible when the associated pdb object is disabled. I've observed this with pymol-py26 1.4-7 installed with fink on a MacBook running 10.6 and with pymol 1.4.1 revision 3968 installed through svn on RHEL 6.1 Notably, earlier revisions (e.g. 3958 and 3945) on RHEL 6.1 work just fine. Recently introduced bug? Andreas -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] distance bug
Ah, indeed, the latest revision 3969 has a correctly working distance command. Thanks Jason. Andreas On 29/09/2011 3:08, Jason Vertrees wrote: Hi Andreas, It was a bug with the invalidation system. I just pushed a fix to source forge. Thanks for bringing this to our attention. Cheers, -- Jason -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity and more. Splunk takes this data and makes sense of it. Business sense. IT sense. Common sense. http://p.sf.net/sfu/splunk-d2dcopy1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
