[PyMOL] ray-tracing cones
Hi All, I am trying to ray trace an empty cone. I can find no way to get an image of the inside of the cone. Does anyone have a work around. Example attached. run test.py cone ray when the ray command is issued the cone disappears from view. robert # # test.py # from pymol import cmd from pymol.cgo import * def cone(name='cone'): o = [] o.extend( [ CONE, 0.0, 0.0, 0.0,# XYZ 1 0.0, 0.0, 1.5,# XYZ 2 0.0, # Radius 1 0.3, # Radius 2 1.0, 0.0, 0.0,# RGB Color 1 0.0, 0.0, 1.0,# RGB Color 2 0.0, 0.0, # Caps 1 & 2 ] ) cmd.load_cgo(o, name) cmd.extend('cone', cone) -- R. Bryn Fenwick, Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA. fenw...@scripps.edu -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk ___ 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
[PyMOL] translation without rotation
Hi, I am trying to translate some object selections and notice that they are undergoing rotations at the same time. I am not sure why this occurs. Can anyone suggest a way to stop this from happening? When I look at the output I can clearly see that a rotation has also occurred. my commands look at bit like: # 1.pdb contains several models # ref.pdb contains a single structure for a common reference load ref.pdb load 1.pdb, 1 load 1.pdb, 2 hide all select bb, resid 342-381 and name ca+c+n and not ref show sticks, bb align 1, ref align 2, ref set state -1 set all_states,1 center all translate [-60.0,0.0,0.0],1 translate [60.0,0.0,0.0], 2 R. Bryn Fenwick -- The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] export frames as pdb
Hi, I have a pdb file that has some models in it. when I open this file they are read in as frames, however now I would like to write them out as frames in a model file. how can i do that? Many thanks, R. Bryn Fenwick -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ 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
[PyMOL] ideal beta-sheet
Hi, I would like to build an ideal beta-sheet fold. Can anyone suggest how to do this with pymol or any other program. I have already tried with the build command, however I am not sure how to proceed once the first strand is built. Many thanks, Bryn -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ 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
[PyMOL] pymol
naming, Hi, I have just been looking at the 1.3 build of pymol that comes from FINK and see that in the build menu that both residues N and Q have the shortcut N. Bryn R. Bryn Fenwick -- Achieve Improved Network Security with IP and DNS Reputation. Defend against bad network traffic, including botnets, malware, phishing sites, and compromised hosts - saving your company time, money, and embarrassment. Learn More! http://p.sf.net/sfu/hpdev2dev-nov ___ 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