[PyMOL] rainbow coloring from the N to C terminus of multiple backbones shown as ribbons
Hi Folks, I have about 2000 pdb files loaded into one session, with their backbones shown as ribbons, that have been aligned by select residues ranging from 15-19 using the align_all command. The problem I have is coloring, right now I have to manually color in rainbow into all of the residues by using the command: set ribbon_color, color name, resi __#__ but the transitions are not smooth. In addition, selecting color/rainbow using the all entry does not do anything to the color. Changing the color manually for each entry, however, works well. I can manually select the color button on each of the pdb entries and select rainbow, but its not feasible to do for 2000 entries. I was wondering if there is an automated way of coloring each ribbon end to end in the same rainbow. Best Regards, Ali -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ 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] rainbow coloring from the N to C terminus of multiple backbones shown as ribbons
Hi Ali, paste this into the PyMOL command line: unset ribbon_color, (*) set ribbon_color, default for name in cmd.get_object_list(): \ cmd.spectrum(selection=name + and polymer) This will do rainbow coloring on each object separately. The ribbon_color setting will override atom colors, that's the reason why selecting color/rainbow from the menu has no effect in your session. Hope that helps. Cheers, Thomas Muhammad Naqvi wrote, On 02/04/13 18:38: Hi Folks, I have about 2000 pdb files loaded into one session, with their backbones shown as ribbons, that have been aligned by select residues ranging from 15-19 using the align_all command. The problem I have is coloring, right now I have to manually color in rainbow into all of the residues by using the command: set ribbon_color, color name, resi __#__ but the transitions are not smooth. In addition, selecting color/rainbow using the all entry does not do anything to the color. Changing the color manually for each entry, however, works well. I can manually select the color button on each of the pdb entries and select rainbow, but its not feasible to do for 2000 entries. I was wondering if there is an automated way of coloring each ribbon end to end in the same rainbow. Best Regards, Ali -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ 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] rainbow coloring from the N to C terminus of multiple backbones shown as ribbons
You are a genius Thomas! On Mon, Feb 4, 2013 at 5:23 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Ali, paste this into the PyMOL command line: unset ribbon_color, (*) set ribbon_color, default for name in cmd.get_object_list(): \ cmd.spectrum(selection=name + and polymer) This will do rainbow coloring on each object separately. The ribbon_color setting will override atom colors, that's the reason why selecting color/rainbow from the menu has no effect in your session. Hope that helps. Cheers, Thomas Muhammad Naqvi wrote, On 02/04/13 18:38: Hi Folks, I have about 2000 pdb files loaded into one session, with their backbones shown as ribbons, that have been aligned by select residues ranging from 15-19 using the align_all command. The problem I have is coloring, right now I have to manually color in rainbow into all of the residues by using the command: set ribbon_color, color name, resi __#__ but the transitions are not smooth. In addition, selecting color/rainbow using the all entry does not do anything to the color. Changing the color manually for each entry, however, works well. I can manually select the color button on each of the pdb entries and select rainbow, but its not feasible to do for 2000 entries. I was wondering if there is an automated way of coloring each ribbon end to end in the same rainbow. Best Regards, Ali -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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
