Re: [PyMOL] bug in selections for "set ribbon_color"
Hi Tom, Settings (thriugh set) apply to objects and not to subsets of objects. Try creating an object from your selection first or change the colors using color. Best, Tsjerk On 9/17/06, Thomas Stout wrote: Has anyone successfully set colors for ribbons via a non-trivial atom selection? The syntax is supposed to be: set ribbon_color, color, selection, state e.g., set ribbon_color, green, /obj01//B should set the ribbon color to green for only chain B of a multi-chain object. However, in practice it appears that setting the ribbon_color applies only to complete objects. Is this a bug or an undocumented expected behavior? Thanks, Tom This email (including any attachments) may contain material that is confidential and privileged and is for the sole use of the intended recipient. Any review, reliance or distribution by others or forwarding without express permission is strictly prohibited. If you are not the intended recipient, please contact the sender and delete all copies. Exelixis, Inc. reserves the right, to the extent and under circumstances permitted by applicable law, to retain, monitor and intercept e-mail messages to and from its systems. - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Tsjerk A. Wassenaar, Ph.D. Groningen Biomolecular Sciences and Biotechnology Institute (GBB) Dept. of Biophysical Chemistry University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands +31 50 363 4336
[PyMOL] center at x,y,z
Hi all, How do I center at a specific coordinate? Can not find any obvious way, by searching the web and manuals. --Björn *** This e-mail may contain confidential information proprietary to Karo Bio AB and is meant for the intended addressee(s) only. Any unauthorized review, use, disclosure or distribution is prohibited. If you have received this message in error, please advise the sender and delete the e-mail and any attachments from your files. Thank you! ***
[PyMOL] problems with vacuum electrostatics
Hello Pymol-users, I have a problem mapping electrostatics on the surface of my pdb file generated using the hhpred modelling method. I load my pdb file and then do actions->generate ->vacuum electrostatics->protein contact potential. Pymol does a number of calculations and generates some objects, but then finally ends up with an error message: Fixing termini and assigning formal charges... Util: Assigning Amber 99 charges and radii... util.sum_formal_charges: sum = 15.0 util.sum_partial_charges: sum = 15.000 Util: Calculating electrostatic potential... ObjectMap: Map created. SelectorMapCoulomb: Total charge is 15.000 for 5455 points (5455 atoms). SelectorMapCoulomb: Evaluating local Coulomb potential for grid (shift=10.00)... Executive: object "hhpred_531_879_mdl_060918_chain_e_pot" created. Setting-Error: unknown color 'hhpred_531_879_mdl_060918_chain_e_pot' I end up with a surface which has green, blue and red patches and not the nice white,blue and red one that I see whenever I try this command on other test pdb files. Does anybody know what is the problem? -Pernille -- Pernille Haste Andersen, M. Sc., Ph D. student Immunological Bioinformatics group, Center for Biological Sequence Analysis, BioCentrum-DTU,Technical University of Denmark, Bld. 208, DK-2800 LYNGBY, DENMARK Tel:(+45) 45252472 E-mail : p...@cbs.dtu.dk
[PyMOL] handedness flip in editing mode
Hi, In editing mode, the handedness flips when I press shift and rotate the object (RotO). This is in effect only during the rotation of the object. Normal rotation (Rota) shows the correct handedness when shift is released. Effectively, the first clicked atom in RotO mode comes to the front (conceptually) and stays so during the rotation event. Setting ribbon_width to 9 shows the color of atoms in front over the color of atoms in the back (using spectrum to differenciate colors) as it should be, but the rotation proceeds in reverse. Should I file a bug report, or am I missing something? Any help will be appreciated. Thanks, Indraneel
[PyMOL] Do presets lock settings?
Hi, I am using pymol v0.99-rc6 on a linux machine. I really like the preset feature (publication, pretty etc.) It's fast and easy when you want to compare structures. However, it seems that when I am using this tool at first, I can't modified the settings after that. For example, if I am using the publication preset, I can not change the loops setting to "smooth loops" anymore. The settings are all locked. Is there a way to avoid this problem??? Thanks, Olivier
