[PyMOL] stick/ribbon rendering not working

2013-01-09 Thread Abhinav Kumar
Hi, I recently upgraded my desktop to Ubuntu 12.10. When I load a pdb in pymol, it comes up with line rendering as usual, but if I try to do a stick or ribbon rendering, it does not do it. In fact the stick operation hides the residue. These are the graphics specifics written by pymol. OpenGL

Re: [PyMOL] stick/ribbon rendering not working

2013-01-11 Thread Abhinav Kumar
: Hi Abhinav, Does this setting help: set cylinder_shader_ff_workaround, 1 If not, can you please send me a screenshot showing the problem? Cheers, -- Jason On Wed, Jan 9, 2013 at 5:40 PM, Abhinav Kumar wrote: Hi, I recently upgraded my desktop to Ubuntu 12.10. When I load a pdb in pymol, it

[PyMOL] new line in label

2013-01-24 Thread Abhinav Kumar
Hi, I want to create a label that has a line break inside it. For example "Asn\n102". Is there a way to do it? The command 'label selection "Asn\n102"' does not work. -- Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 -

Re: [PyMOL] Bugfix release 1.7.0.5

2014-05-21 Thread Abhinav Kumar
this? Coot and rasmol are not affected by this Ubuntu upgrade. Thanks, Abhinav __ Abhinav Kumar, Ph.D. The Joint Center for Structural Genomics MS99, SLAC National Accelerator Laboratory 2575 Sand Hill Rd, Menlo Park, CA 94025 (650) 926-2992 On 05/13/2014 10

Re: [PyMOL] Bugfix release 1.7.0.5

2014-05-21 Thread Abhinav Kumar
Thanks Clotilde again. I switched the graphics card driver and it has fixed the problem. The switch I made was from Nouveau display driver to Nvidia dreiver. Thanks, Abhinav __ Abhinav Kumar, Ph.D. The Joint Center for Structural Genomics MS99, SLAC National

[PyMOL] Default color scheme for objects

2008-11-25 Thread Abhinav Kumar
Hi, When you load in several pdb files in pymol, the objects get colored by a default color scheme, e.g. first green, second cyan, third magenta etc. Where can I get a ordered list of these color names? Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural G

[PyMOL] Showing conserved residues

2009-01-29 Thread Abhinav Kumar
Hi, Is there someway to select and show conserved residues when a bunch of superimposed structures are loaded into Pymol? And if so, can identical and similar residues be selected separately? -- Thanks Abhinav Stanford Synchrotron Radiation Laboratory Joint Center for Structural Genomics

[PyMOL] Saving figures for publication

2009-03-13 Thread Abhinav Kumar
Hi, I need to make figures in tiff format with at least 600 dpi resolution as required by the journal. The default resolution in Pymol figures is 72. Is there a simple way to increase the resolution (and save it in tiff format)? Alternatively, I can 'convert' from png to tiff afterwards -- T

Re: [PyMOL] Saving figures for publication

2009-03-13 Thread Abhinav Kumar
quired 600 dpi. Roger Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@mail.colgate.edu -Original Message----- From: Abhinav Kumar Da

RE: [PyMOL] RE: Pymol and Movie

2002-02-13 Thread Abhinav Kumar
I tried the gifmerge which worked just fine. Thanks Abhinav -Original Message- From: Daan van Aalten [mailto:d...@davapc1.bioch.dundee.ac.uk] Sent: Wednesday, February 13, 2002 1:50 PM To: DeLano, Warren Cc: Abhinav Kumar; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] RE