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 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
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
[PyMOL] 1st Call For Papers, 19th Annual Tcl/Tk Conference 2012
20'th Annual Tcl/Tk Conference (Tcl'2013) http://www.tcl.tk/community/tcl2013/ September 23 - 27, 2013 Bourbon Orleans Hotel New Orleans, Louisiana, USA Important Dates: Abstracts and proposals due June 22, 2013 Notification to authors August 5, 2013 Author materials due September 2, 2013 Tutorials Start September 23, 2013 Conference starts September 25, 2013 Email Contact:tclconfere...@googlegroups.com Submission of Summaries Tcl/Tk 2013 will be held in New Orleans, Louisiana, USA from September 23 - 27, 2013. The program committee is asking for papers and presentation proposals from anyone using or developing with Tcl/Tk (and extensions). Past conferences have seen submissions covering a wide variety of topics including: * Scientific and engineering applications * Industrial controls * Distributed applications and Network Managment * Object oriented extensions to Tcl/Tk * New widgets for Tk * Simulation and application steering with Tcl/Tk * Tcl/Tk-centric operating environments * Tcl/Tk on small and embedded devices * Medical applications and visualization * Use of different programming paradigms in Tcl/Tk and proposals for new directions. * New areas of exploration for the Tcl/Tk language Submissions should consist of an abstract of about 100 words and a summary of not more than two pages, and should be sent as plain text to no later than August 5, 2013. Authors of accepted abstracts will have until September 2, 2013 to submit their final paper for the inclusion in the conference proceedings. The proceedings will be made available on digital media, so extra materials such as presentation slides, code examples, code for extensions etc. are encouraged. Printed proceedings will be produced as an on-demand book at lulu.com The authors will have 25 minutes to present their paper at the conference. The program committee will review and evaluate papers according to the following criteria: * Quantity and quality of novel content * Relevance and interest to the Tcl/Tk community * Suitability of content for presentation at the conference Proposals may report on commercial or non-commercial systems, but those with only blatant marketing content will not be accepted. Application and experience papers need to strike a balance between background on the application domain and the relevance of Tcl/Tk to the application. Application and experience papers should clearly explain how the application or experience illustrates a novel use of Tcl/Tk, and what lessons the Tcl/Tk community can derive from the application or experience to apply to their own development efforts. Papers accompanied by non-disclosure agreements will be returned to the author(s) unread. All submissions are held in the highest confidentiality prior to publication in the Proceedings, both as a matter of policy and in accord with the U. S. Copyright Act of 1976. The primary author for each accepted paper will receive registration to the Technical Sessions portion of the conference at a reduced rate. Other Forms of Participation The program committee also welcomes proposals for panel discussions of up to 90 minutes. Proposals should include a list of confirmed panelists, a title and format, and a panel description with position statements from each panelist. Panels should have no more than four speakers, including the panel moderator, and should allow time for substantial interaction with attendees. Panels are not presentations of related research papers. Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather sessions (BOFs) are available on a first-come, first-served basis starting in August 5, 2013. Specific instructions for reserving WIP and BOF time slots will be provided in the registration information available in June 3, 2013. Some WIP and BOF time slots will be held open for on-site reservation. All attendees with an interesting work in progress should consider reserving a WIP slot. Registration Information More information on the conference is available the conference Web site (http://www.tcl.tk/community/tcl2013/) and will be published on various Tcl/Tk-related information channels. To keep in touch with news regarding the conference and Tcl events in general, subscribe to the tcl-announce list. See: http://code.activestate.com/lists/tcl-announce to subscribe to the tcl-announce mailing list. Conference Committee Clif Flynt Noumena CorpGeneral Chair, Website Admin Andreas Kupries ActiveState Software Inc. Program Chair Gerald Lester KnG Consulting, LLC Site/Facilities Chair Arjen MarkusDeltares Brian Griffin Mentor Graphics Cyndy Lilagan Nat. Museum of Health & Medicine, Chicago Donal Fellows University of Manchester Jeffrey Hobbs ActiveState Software Inc. Kevin Kenny GE Global Research Center Larry
[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
[PyMOL] problem setting up morph under eMovie
My institution a subscription to incentive PyMol. In the past, I have used the morph that appeared under the list of eMovie commands but now it does not appear. I am not sure what i am missing: a vaild rigimol file, the wrong version (currently using Version 1.5.0.4). Regardless I also need instructions for how to embed the morph in the list of commands. Any help would be greatly appreciated. Thanks -- 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
[PyMOL] post to list
-- 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