[PyMOL] Question about pymol movies
Hi Pymol Users, I need your help with an issue related to movie in pymol. I know how to change the representation of the molecule that appears in my movie at a given frame but I don't find the way to change the representation of just a given part of such molecule, lets say make some residues become partially transparent or change color while the rest keep the same appearance. I am following section "Motions and Representations" in this tutorial https://pymolwiki.org/index.php/MovieSchool_5 but it doesn't work. Once I change the representation of the chosen residues, they remain with the new aspect along the whole movie... Could somebody give me a clue on how to proceed? Thank you very much in advance! Kind regards, Miguel -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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] Segmentation fault
Thanks for the feedback, Folmer! I am using CentOS. I already used --use-msgpackc=no and it did not improve. gcc --version gives me 4.8.5 (I cannot update more). Do you think it would be worth it to install gcc 4.9? On the install page there was said that a regression to 4.4 could work, but I don’t know. Anyone else using CentOS having problems with pymol installation? Thanks, João On Wed, Mar 29, 2017 at 10:35 AM, Folmer Fredslund wrote: > Hi João, > > On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9 > and "--use-msgpackc=no" I get a working pymol with revision 4170. > > Have you tried creating a new user and test pymol from that account? That > should help you identify if it is solely a problem with your own account. > > HTH, > Folmer > > > On 2017-03-28 03:15, João M. Damas wrote: > > Nobody experiencing the same issues? Any tips on what I may be doing wrong > on the installation? > > João > > On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas > wrote: > >> Dear all, >> >> I started experiencing segmentation fault on a pymol that I had installed >> through the omnia channel on conda. >> >> Then, I decided to install from scratch using this recipe: >> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN >> >> Still getting the segmentation fault, so maybe something changed in my >> system and it's conflicting with? >> >> The segmentation fault is not on launching PyMOL, but rather when I do >> stuff: loading a PDB file, building a fragment. Like this: >> >> ``` >> ./pymol: line 3: 28505 Segmentation fault "/usr/bin/python2.7" >> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@" >> ``` >> >> Curiously, when I load a 1.740 session (.pse file I had saved), it works >> (no segmentation fault), I can even perform commands like select and stuff, >> and they work. If I load a more recent 1.803 session, it also seg faults: >> >> ``` >> Executive: Loading version 1.803 session... >> ./pymol: line 3: 29221 Segmentation fault "/usr/bin/python2.7" >> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@" >> ``` >> >> Any clues? Am I doing something wrong? >> >> Thanks, >> João >> >> -- >> João M. Damas >> PhD Student >> Protein Modelling Group >> ITQB-UNL, Oeiras, Portugal >> Tel:+351-214469613 <21%20446%209613> >> > > > > -- > João M. Damas > PhD Student > Protein Modelling Group > ITQB-UNL, Oeiras, Portugal > Tel:+351-214469613 <21%20446%209613> > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > ___ > 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 > > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > 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 > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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] Segmentation fault
Hi João, Before diving into the hassle of installing additional compilers (which probably won't make a difference) I recommend to get familiar with a debugger like gdb and obtain a stack trace of the crash. To compile PyMOL with debug symbols, do export DEBUG=1 before running setup.py. Then run PyMOL (actually: python) with gdb. There is a bit of a learning curve to get familiar with gdb, but considering that you already spend time on this problem and are willing to spend more, I think it's worthwhile. Cheers, Thomas On 11 Apr 2017, at 19:08, João M. Damas wrote: > Thanks for the feedback, Folmer! > > I am using CentOS. I already used --use-msgpackc=no and it did not improve. > gcc --version gives me 4.8.5 (I cannot update more). Do you think it would be > worth it to install gcc 4.9? On the install page there was said that a > regression to 4.4 could work, but I don’t know. > > Anyone else using CentOS having problems with pymol installation? > > Thanks, > João > > > On Wed, Mar 29, 2017 at 10:35 AM, Folmer Fredslund wrote: > Hi João, > > On Ubuntu 16.04 (you didn't mention what you were running) with gcc-4.9 and > "--use-msgpackc=no" I get a working pymol with revision 4170. > > Have you tried creating a new user and test pymol from that account? That > should help you identify if it is solely a problem with your own account. > > HTH, > Folmer > > > On 2017-03-28 03:15, João M. Damas wrote: >> Nobody experiencing the same issues? Any tips on what I may be doing wrong >> on the installation? >> >> João >> >> On Fri, Mar 17, 2017 at 4:08 PM, João M. Damas wrote: >> Dear all, >> >> I started experiencing segmentation fault on a pymol that I had installed >> through the omnia channel on conda. >> >> Then, I decided to install from scratch using this recipe: >> https://pymolwiki.org/index.php/Linux_Install#Get_latest_source_from_SVN >> >> Still getting the segmentation fault, so maybe something changed in my >> system and it's conflicting with? >> >> The segmentation fault is not on launching PyMOL, but rather when I do >> stuff: loading a PDB file, building a fragment. Like this: >> >> ``` >> ./pymol: line 3: 28505 Segmentation fault "/usr/bin/python2.7" >> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@" >> ``` >> >> Curiously, when I load a 1.740 session (.pse file I had saved), it works (no >> segmentation fault), I can even perform commands like select and stuff, and >> they work. If I load a more recent 1.803 session, it also seg faults: >> >> ``` >> Executive: Loading version 1.803 session... >> ./pymol: line 3: 29221 Segmentation fault "/usr/bin/python2.7" >> "/data/joao/maindisk/software/pymol-svn/modules/pymol/__init__.py" "$@" >> ``` >> >> Any clues? Am I doing something wrong? >> >> Thanks, >> João >> >> -- >> João M. Damas >> PhD Student >> Protein Modelling Group >> ITQB-UNL, Oeiras, Portugal >> Tel:+351-214469613 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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 - 24th Annual Tcl/Tk Conference (Tcl'2017)
Hello pymol-users, fyi ... 24th Annual Tcl/Tk Conference (Tcl'2017) http://www.tcl.tk/community/tcl2017/ October 16 - 20, 2017 Crowne Plaza Houston River Oaks 2712 Southwest Freeway, 77098 Houston, Texas, USA Important Dates: Abstracts and proposals due August 21, 2017 Notification to authors August 28, 2017 WIP and BOF reservations open July 24, 2017 Author materials due September 25, 2017 Tutorials Start October 16, 2017 Conference starts October 18, 2017 Email Contact:tclconfere...@googlegroups.com Submission of Summaries Tcl/Tk 2017 will be held in Houston, Texas, USA from October 16, 2017 to October 20, 2017. 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 tclconfere...@googlegroups.com no later than August 21, 2017. Authors of accepted abstracts will have until September 25, 2017 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 30 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 July 24, 2017. Specific instructions for reserving WIP and BOF time slots will be provided in the registration information available in July 24, 2017. 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/tcl2017/) 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 * Alexandre Ferrieux * Andreas KupriesSUSE * Arjen Markus Deltares * Brian Griffin Mentor Graphics - A Siemens Business * Clif Flynt Noumena Corp * Gerald Lester KnG Consulting LLC * Joe Mistachkin Mistachkin Systems * Ronald Fox CAEN Technologies NSCL @ Michigan State University * Steve Landers Dig
[PyMOL] plugin manager
Hi! I needed to install PyTMs but am unable to do so. I can't find the plugin manager. In the menu, after the wizard I have 'help' not 'plugins'. I installed the educational version of MacPyMOL in around Aug/Sep 2015. Looking forward to your help, Regards, Raag -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot___ 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] plugin manager
Hi Raag, You need to run MacPyMOL with the "X11 Hybrid" interface, see: https://pymolwiki.org/index.php/MAC_Install#X11_Hybrid Cheers, Thomas On 12 Apr 2017, at 08:02, Raag Saluja wrote: > Hi! > > I needed to install PyTMs but am unable to do so. I can't find the plugin > manager. In the menu, after the wizard I have 'help' not 'plugins'. > > I installed the educational version of MacPyMOL in around Aug/Sep 2015. > > Looking forward to your help, > Regards, > Raag -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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
