[PyMOL] VASCo plug-in Tk error
Hi everybody, I am trying to run VASCo (VASCo-Modules-1.0.2) as plug-in (ppixplugin_v077.py) on my MacPyMol version 1.6.9.0. Mac version 10.9.2. Maybe someone knows how to fix the problem? Thanks in advance for your help! Errormessage: Error: 1 class '_tkinter.TclError' Exception in Tk callback Function: bound method Ppix_db_file.fetchFileName of pmg_tk.startup.ppixplugin_v077.Ppix_db_file instance at 0x10af0b0e0 (type: type 'instancemethod') Args: () Traceback (innermost last): File /sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py, line 1753, in __call__ return apply(self.func, args) File /Users/timshulte/.pymol/startup/ppixplugin_v077.py, line 3213, in fetchFileName self.initialize_surface_view(ppix_filename) File /Users/timshulte/.pymol/startup/ppixplugin_v077.py, line 3253, in initialize_surface_view self.widget.create_prop_widgets(properties_to_show) File /Users/timshulte/.pymol/startup/ppixplugin_v077.py, line 2706, in create_prop_widgets self.create_color_widges(property_key=key,parent_frame=self.scroll) File /Users/timshulte/.pymol/startup/ppixplugin_v077.py, line 2840, in create_color_widges self._descript.grid(column=property_key, row=0, padx=20, pady=20) File string, line 1, in grid None File /sw/lib/python2.7/lib-tk/Tkinter.py, line 1963, in grid_configure + self._options(cnf, kw)) class '_tkinter.TclError': cannot use geometry manager grid inside .4477443032.4478501520.4478541976.4478557288.4478557432.4478557504.4478588256.4478588688.4478588760.4478589408 which already has slaves managed by pack -- ___ 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] How to draw clashes in pymol - integration/plug-in of Molprobity in PyMol???
Hej everybody, my question is related to this post. I am just analyzing a structure and really like the way Molprobity puts out information about hydrogen bonds and vdW contacts and so on. It is also possible to take advantage of this analysis in phenix during/after refinement, because Coot provides a graphical interface for visualization of the Molprobity output - however, Coot is not my favorite program for making nice figures. So I just wonder whether it might be of general interest to the pymol community if someone would write a plug-in to integrate the Molprobity output in PyMol? I can definitely not do it, but maybe this could be an interesting feature request to the PyMol developers? All the best, Tim Am 30/08/14 01:53, schrieb Robert Immormino: Hi Bondurant, I really like the merging of the graphic beauty of pymol with the detailed depictions of reduce and probe. I have a method that is a bit clunky for doing what you ask, but I don't know if it ever made it to the mainstream in MolProbity. The caveat of wanting to work with a ligand makes it a bit harder to explain so my apologies in advance if things aren't 100% clear but here goes 1. Make sure you have a reduce definition file for your ligand. If the ligand had been deposited in the PDB before ~2012 then the reduce_wwPDB_het_dict file found (http://kinemage.biochem.duke.edu/software/reduce.php) should have it, otherwise here's an example: RESIDUE ACP 11 CONECT P 4 O1 O2 O3 O4 CONECT O1 1 P CONECT O2 1 P CONECT O3 1 P CONECT O4 2 PC1 CONECT C1 3 O4 O5 C2 CONECT O5 1 C1 CONECT C2 4 C1 HC1 HC2 HC3 CONECT HCH11 C2 CONECT HCH21 C2 CONECT HCH31 C2 END HETACP 8 HETNAM ACP ACETYL PHOSPHATE FORMUL ACPC2 H3 O5 P1 2- 2. download the reduce and probe executables also from http://kinemage.biochem.duke.edu/ 3. run reduce make sure to use the -DB flag to input your ligand dictionary 4. run probe with a command something like: probe -both chaina 88 (ATOM_OG1 | ATOM_HG1) chainx 1 CheY_A88T_AcP_H.pdb Where chain A in this case is the protein and the hydroxyl of Thr 88 is the only relevant interacting group with chain X the ligand. 5. convert the probe output to a python script to render the cgo objects in pymol using the attached perl script. ./probe_to_cgo [input probe dots] [output pymol cgo] 6. use the run command in pymol to execute the python script and draw the cgo output. If this all works the first go then amazing! If not I can try to help get things working, but it's been a few years since I last used these tools. Best of Luck! -bob On Fri, Aug 29, 2014 at 10:30 AM, Bondurant bondurant...@gmail.com mailto:bondurant...@gmail.com wrote: Hello community, I would like to draw a figure similar to this one http://www.cell.com/cms/attachment/615980/4968633/gr1.jpg showing the clashes between a potential ligand and the protein. The only way i know how to do this in pymol is using the show_bumps plugin, but i don't really like the red disks format. Could anyone tell me how i could easily draw something similar to those red spikes from the example to represent the clashes in pymol or any other program? I'm able to do it using molprobity and kinemage, but there's no much possibilities for editing and to get it in printing quality. Thanks -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net mailto: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 -- Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ ___ 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-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] Editing of the pdb structure
Dear James, I agree with Joao, for fast and dirty minimisation you might try the program Chimera or VegaZZ. If you just wanna have an energy-minimized small molecule the Prodrg server is the way to go. Cheers, Tim Von: João Rodrigues [anar...@gmail.com] Gesendet: Freitag, 27. Januar 2012 09:56 Bis: James Starlight Cc: pymol-users@lists.sourceforge.net Betreff: Re: [PyMOL] Editing of the pdb structure Dear James, As someone has told you already, Pymol is a visualization tool, not a modelling suite. I guess you would be better off using something like AMBERTOOLS or MODELLER, depending on what you want to model, or any other real simulation/modelling package otherwise your results are very weak... My opinion only. João [...] Rodrigues http://nmr.chem.uu.nl/~joao No dia 27 de Janeiro de 2012 09:50, James Starlight jmsstarli...@gmail.commailto:jmsstarli...@gmail.com escreveu: Arne, Thomas Thanks alot. Bond works finw I'd like just to ask what about geometry optimisation of the new structure E.g I want create 5memb imidazole ring where the 2 adj atoms are apart from 1.5 A from each other. When I've create new bond by bond command new ring look like 6memb ( like benzol) because of long distance between adj atoms. How I could optimise geometry of the new mollecule? Have pymol some built-in functions like conformational search be means of monte carlo or energy minimisation ? James 2012/1/27 Thomas Holder spel...@users.sourceforge.netmailto:spel...@users.sourceforge.net On 01/27/2012 09:11 AM, James Starlight wrote: Dear PyMol users! I need to create NEW covalent bond between two adjacent atoms. How this could be done in PyMOl? you could have guessed it: http://pymolwiki.org/index.php/Bond :-) The atoms must both be within the same object. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.netmailto: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 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ 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] Movie to export
Hi, Quick time player 7 pro does a great job for me. Cheers Tim Am 11/8/11 9:54 PM, schrieb Troels Emtekær Linnet: Hi. I have made a nice little movie in Pymol. 1500 frames. So now I am wondering what is the best method to export? At the moment I do export to .png with ray tracing each image. set ray_trace_frames = 1 That takes a long time. And what program should I use to pack them together? The easy wasy? Can it be done faster with the MPEG method? Best Troels Troels Emtekær Linnet Slotsvej 2 4300 Holbæk Mobil: +45 60210234 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 ___ 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 -- RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1___ 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] movie enhancement feature request...
Yes, that is exactly what I wanted. Perfect. Thank you very much. Am 9/14/11 5:59 PM, schrieb Jason Vertrees: Hi Tim, I love pymol for creating high quality figures and analysing my structures. But creating movies in pymol is rather tedious... CCP4mg seems to be much easier to use for creating movies, you just have to save a scene and CCP4mg interpolates between the created scenes. Is there a plan to include such a feature in pymol as well? It would simplify the structural biologist`s life enormously. Thanks for writing. PyMOL has had this capability for years--and it's really simple. You define scenes from the command line, using hot keys, or through the Scene menu. After your scenes are defined you can scroll through them with PgUp/PgDn or through the menus (Scene Next/Previous). Here's a small intro to get you started: # create something to make a movie from fetch 1rx1, async=0 # turn on scene buttons set scene_buttons # store a scene; same as Ctrl-PgDn on the # keyboard or Scene Append from menus scene 001, append orient # store a scene; same as Ctrl-PgDn on the # keyboard or Scene Append from menus scene 002, append # move the camera around orient i. 40-42 show sticks, i. 40-42 # store scene scene 003, append # move the camera around, change # representation turn x, 45 as cartoon # store scene scene 004, append # go to the first scene scene 001 Now just hit PgUp/PgDn to automatically interpolate between scenes. Movie Program Scene Loop ... will automatically program the movie for you (click the play button after you do this). If you have Incentive PyMOL then File Save Movie MPEG will even dump the movie to an MPEG for you. PyMOL will always smoothly transition from scene to scene even if you interrupt the transition. All of the above could have just as easily been done using the mouse: in PyMOL you can create movies without even touching the keyboard if you want. PyMOL also gives you scene buttons to click on and (right-click on). Here's a more in depth, if slightly outdated, tutorial: http://www.pymolwiki.org/index.php/MovieSchool Cheers, -- Jason -- BlackBerryreg; DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerryreg; mobile platform with sessions, labs more. See new tools and technologies. Register for BlackBerryreg; DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 ___ 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
