Re: [PyMOL] GUI to improve interaction between user and PyMOL
Sorry for being rude, it was not meant in that way. I was just puzzled by the fact, that you would be graded higher if you don't use the command line. That is just weird. Back to the question. Suhaila, you should try to explore the action button. First get a protein, which is good to illustrate. Go to the menu: Plugin-PDB Loader Service. Enter: 1hpu (Or write in command: fetch 1hpu ) :-) Then go to the A (Action) button in the right menu. Press: preset - ligand sites - cartoon Try some of the presets. They are very good! If you want to find some polar contacts. Select your residue by clicking it: Action - find - polar contacts - Then something from the menu I hope that helps! Best Troels 2012/3/23 Suhaila Haji Mohd Hussin bell_beaut...@hotmail.com OK. It does sound pretty weird prolly because the way I asked isn't precise. We plot predicted contacts that can be viewed in various ways. So it'd be better to create a GUI select menu or something like that for user's ease of interacting with our project. Suhaila. -- From: tlin...@gmail.com Date: Thu, 22 Mar 2012 22:14:39 +0100 CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] GUI to improve interaction between user and PyMOL That is seriously the strangest thing I ever heard about... The GUI is for the small fast thing to do. Why just don't press all button and see? It can only take a little time. Or google: pymol + name of button That should give you an answer... The command line is where the power is. Use that. /Troels 2012/3/22 Suhaila Haji Mohd Hussin bell_beaut...@hotmail.com Hello everyone. Is there any useful online reference that can be shared for me to learn how to add GUI executed by Python script? I know PyMOL can visualize the protein just by typing in on PyMOL command but my supervisor will grade my group project higher if we can make it more interactive where the user can just use a mouse to click button or something and less typing on command. Best regards, *Suhaila* -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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] GUI to improve interaction between user and PyMOL
Hi Suhaila, Correct me if I'm wrong but you want create *new* GUI elements for pymol to enhance your application, right? To my knowledge, there is not a great tutorial on this, but I can give you some pointers to plugins that do this currently and hopefully you can backfill some knowledge. The first point I should make though is that, as far as I know, you *cannot* modify the existing PyMol windows, that is, you can't add an item to the menu you get when you right click on a protein or make it so there are additional per object menus on the right side of the screen for your application. Generally, for PyMol, your plugin interface is written using Tkinter, which is widely documented across the internet ( http://wiki.python.org/moin/TkInter ). http://www.pymolwiki.org/index.php/Plugins_Tutorial provides a simple example of a plugin with a graphical interface. The __init__ adds your plugin to the menu bar in PyMol and tells PyMol what to execute when you click on the button. From there, it is just Tkinter with python and pymol scripting. The only pymol plugin I currently use with a graphical interface is the Autodock plugin: https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/plugins/autodock_plugin.py It's a pretty complex piece of code, but it is a nice plugin that seems highly reliable, so understanding looking at how it does things can probably help you solve any issues you have along the way. There are other plugins that you can find by browsing the pymolwiki that also use graphical elements and may also be helpful. -David On Thu, Mar 22, 2012 at 4:39 PM, Suhaila Haji Mohd Hussin bell_beaut...@hotmail.com wrote: Hello everyone. Is there any useful online reference that can be shared for me to learn how to add GUI executed by Python script? I know PyMOL can visualize the protein just by typing in on PyMOL command but my supervisor will grade my group project higher if we can make it more interactive where the user can just use a mouse to click button or something and less typing on command. Best regards, Suhaila -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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] GUI to improve interaction between user and PyMOL
OK. It does sound pretty weird prolly because the way I asked isn't precise. We plot predicted contacts that can be viewed in various ways. So it'd be better to create a GUI select menu or something like that for user's ease of interacting with our project. Suhaila. From: tlin...@gmail.com Date: Thu, 22 Mar 2012 22:14:39 +0100 CC: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] GUI to improve interaction between user and PyMOL That is seriously the strangest thing I ever heard about... The GUI is for the small fast thing to do.Why just don't press all button and see?It can only take a little time. Or google: pymol + name of buttonThat should give you an answer... The command line is where the power is.Use that. /Troels 2012/3/22 Suhaila Haji Mohd Hussin bell_beaut...@hotmail.com Hello everyone. Is there any useful online reference that can be shared for me to learn how to add GUI executed by Python script? I know PyMOL can visualize the protein just by typing in on PyMOL command but my supervisor will grade my group project higher if we can make it more interactive where the user can just use a mouse to click button or something and less typing on command. Best regards, Suhaila -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure ___ 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 -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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] execute a set of pml files on a set of pse files iteratively and saving without opening the Pymol GUI
Hi everyone, I have a set of (240 files) of pse files like 1.pse 2.pse . . . 240.pse I also have a set of(240 files) pml files like 1.pml 2.pml . . . 240.pml I want execute the pml files iteratively on the corresponding pse files and save the new pse files as 1new.pse,2new.pse, so on. from the command line of pymol(without opening the GUI). Can anyone suggest me a way to do this? Thank you Sajeewa -- This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure___ 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] execute a set of pml files on a set of pse files iteratively and saving without opening the Pymol GUI
Hi Sajeewa,
paste this into a python script (script.py):
from pymol import cmd
for i in range(1, 240+1):
cmd.reinitialize()
cmd.load('%d.pse' % i)
cmd.do('@%d.pml' % i)
cmd.sync()
cmd.save('%dnew.pse' % i)
Run it with PyMOL in batch mode:
pymol -cqr script.py
See also: http://pymolwiki.org/index.php/Command_Line_Options
Cheers,
Thomas
On 03/21/2012 08:48 AM, Sajeewa Pemasinghe wrote:
Hi everyone,
I have a set of (240 files) of pse files like
1.pse
2.pse
.
.
.
240.pse
I also have a set of(240 files) pml files like
1.pml
2.pml
.
.
.
240.pml
I want execute the pml files iteratively on the corresponding pse files
and save the new pse files as 1new.pse,2new.pse, so on. from the command
line of pymol(without opening the GUI). Can anyone suggest me a way to
do this?
Thank you
Sajeewa
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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Re: [PyMOL] Superimposing 2 or more Selections PyMOL GUI
Hi Spyros, In cases like these, I think it's usually best to use colours for the selections and for the overlap: color cyan, selection1 color yellow, selection2 color hotpink, selection1 and selection2 Hope it helps, Tsjerk On Tue, Jul 12, 2011 at 1:14 AM, Spyros Charonis s.charo...@gmail.com wrote: Hello PyMOLers, A visualization query: I have a PDB structure of a GPCR to which I have added two selections, one where I highlight certain motif sequences extracted from a database, and the second where I highlight a set of residues that bind ligands. Because I wish to determine if I can correlate the database motifs with ligand-binding residues, what I would like is some way of superimposing (if possible) one selection onto the other. I would color-code the selections (if possible, again) so that I could see if one was on top of the other in 3D or if they occur at different regions of the protein. Creating selections the default way places pixel-size pink dots on the structure, so I was wondering if there is some way to control this for more complex visualization tasks? Is there a way to color-code my selections, and visualize them simultaneously on the structure to see if there is any overlap? Many thanks for your time! Spyros -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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] Superimposing 2 or more Selections PyMOL GUI
Hi Spyros, Creating selections the default way places pixel-size pink dots on the structure, so I was wondering if there is some way to control this for more complex visualization tasks? set active_selections, off set auto_show_selections, off both seem to hide the pixels, but I'm not sure which one is the better to use. To find such settings, I can recommend 'grepset' from the PyMOLWiki: http://pymolwiki.org/index.php/Grepset Is there a way to color-code my selections, and visualize them simultaneously on the structure to see if there is any overlap? See Tsjerk's reply. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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] Superimposing 2 or more Selections PyMOL GUI
Hi Spyros, Because I wish to determine if I can correlate the database motifs with ligand-binding residues, what I would like is some way of superimposing (if possible) one selection onto the other. I would color-code the selections (if possible, again) so that I could see if one was on top of the other in 3D or if they occur at different regions of the protein. If you're using PyMOL for the alignments, then please understand the differences between align, super and cealign. Lots of documentation on this can be found on these pages: http://www.pymolwiki.org/index.php/Align; http://www.pymolwiki.org/index.php/Super; http://www.pymolwiki.org/index.php/Cealign. Creating selections the default way places pixel-size pink dots on the structure, so I was wondering if there is some way to control this for more complex visualization tasks? You can modify the indicators, the pixel-size pink dots, and their activity just a little (see selection_round_points, and selection_overlay settings). But this is best done by color-coding your selected atoms, not by modifying the indicator dots. Is there a way to color-code my selections, and visualize them simultaneously on the structure to see if there is any overlap? The most flexible way to do this is as Tsjerk suggested: changing the colors, or representations of your selections. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 ___ 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] Superimposing 2 or more Selections PyMOL GUI
Hi Spyros, Thank you for the links, this documentation is helpful! I am not actually creating alignments, I just choose the Display = Sequence option from the external GUI menu to get the protein sequence of my PDB structure. I was meaning to ask - for a couple of PDB structures when PyMOL loads the structure and the sequence is displayed, sometimes several parts of it are missing. I attach a small image as an example (there are only 5 letters between 226 and 271), I have checked the PDB server and the sequence page has the full information. Is this skipping parts of sequence something internal to PyMOL? The sequence viewer skips over incomplete residues or missing data. That is, if a residue is missing from the sequence viewer then data are missing from the PDB file. For 3p0g, you will notice that the sequence viewer goes from residue 227 to 266. This is because there's a break in the chain in the PDB file; Lines 2326 and 2327 from 3p0g.pdb show: ATOM 1631 NZ LYS A 227 30.660 30.248 18.940 1.00101.97 N ATOM 1632 N LEU A 266 23.034 24.451 21.103 1.00132.21 N which show residue 227 being right before residue 266. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- AppSumo Presents a FREE Video for the SourceForge Community by Eric Ries, the creator of the Lean Startup Methodology on Lean Startup Secrets Revealed. This video shows you how to validate your ideas, optimize your ideas and identify your business strategy. http://p.sf.net/sfu/appsumosfdev2dev ___ 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] Superimposing 2 or more Selections PyMOL GUI
Hello PyMOLers, A visualization query: I have a PDB structure of a GPCR to which I have added two selections, one where I highlight certain motif sequences extracted from a database, and the second where I highlight a set of residues that bind ligands. Because I wish to determine if I can correlate the database motifs with ligand-binding residues, what I would like is some way of superimposing (if possible) one selection onto the other. I would color-code the selections (if possible, again) so that I could see if one was on top of the other in 3D or if they occur at different regions of the protein. Creating selections the default way places pixel-size pink dots on the structure, so I was wondering if there is some way to control this for more complex visualization tasks? Is there a way to color-code my selections, and visualize them simultaneously on the structure to see if there is any overlap? Many thanks for your time! Spyros -- All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2___ 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 call the align command without opening Pymol GUI window
Hi Li, I created a small python script testAlign.py with the following 3 lines as its content: cmd.fetch(1cll 1ggz, async=0) rmsd = cmd.align(1cll, 1ggz)[0] print RSMD for aligning 1cll to 1ggz is: , rmsd This fetches two PDBs, aligns them and reports their RMSD. Now, just run pymol -cq testAlign.py and you should see RSMD for aligning 1cll to 1ggz is: 3.85577607155 as the last line of output. Cheers, -- Jason On Sun, Sep 12, 2010 at 6:09 PM, Li Xue me.li...@gmail.com wrote: Hello all, Does someone happen to know how call the pymol commands (for example, align) without opening Pymol GUI window? Thanks. -- Xue, Li Bioinformatics and Computational Biology program Computer Science Iowa State University Ames, IA 50010 - USA Tel: 1-515-450-7183 Email: me.li...@gmail.com -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing http://p.sf.net/sfu/novell-sfdev2dev ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing http://p.sf.net/sfu/novell-sfdev2dev ___ 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] not getting pymol gui
Hai all, Few days back, i wrote a mail regarding the problem of not getting pymol gui while starting pymol. The folllowing are the errors it throws when i give pymol in command line. freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer' This may hurt performance. PyMOL(TM) Molecular Graphics System, Version 1.1r2pre. Copyright (C) 2008 by DeLano Scientific LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. Other Major Authors and Contributors: Ralf W. Grosse-Kunstleve, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at http://www.pymol.org;. Enter help for a list of commands. Enter help command-name for information on a specific command. Hit ESC anytime to toggle between text and graphics. OpenGL graphics engine: GL_VENDOR: Mesa Project GL_RENDERER: Software Rasterizer GL_VERSION: 1.4 (2.1 Mesa 7.3-devel) Traceback (most recent call last): File /usr/lib/python2.5/site-packages/pymol/__init__.py, line 400, in launch_gui __import__(self.invocation.options.gui) File /usr/lib/python2.5/site-packages/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /usr/lib/python2.5/site-packages/pmg_tk/PMGApp.py, line 28, in module from Tkinter import * File /usr/lib/python2.5/lib-tk/Tkinter.py, line 38, in module import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/local/chimera/lib/libtk8.5.so: cannot restore segment prot after reloc: Permission denied Detected 2 CPU cores. Enabled multithreaded rendering. Kindly suggest me what is going wrong, Thanks in advance, Bala
Re: [PyMOL] not getting pymol gui
Bala, Based on that error, it appears that Chimera's Tk installation is intefering with PyMOL's ability to get at its own Tk installation. Are any PYTHON, TCL, or TK environment variables defined in your path? If so, then they may need to be cleared out in order to run PyMOL. Cheers, Warren From: Bala subramanian [mailto:bala.biophys...@gmail.com] Sent: Friday, March 13, 2009 5:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] not getting pymol gui Hai all, Few days back, i wrote a mail regarding the problem of not getting pymol gui while starting pymol. The folllowing are the errors it throws when i give pymol in command line. freeglut (pymol): Unable to create direct context rendering for window 'PyMOL Viewer' This may hurt performance. PyMOL(TM) Molecular Graphics System, Version 1.1r2pre. Copyright (C) 2008 by DeLano Scientific LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. Other Major Authors and Contributors: Ralf W. Grosse-Kunstleve, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at http://www.pymol.org;. Enter help for a list of commands. Enter help command-name for information on a specific command. Hit ESC anytime to toggle between text and graphics. OpenGL graphics engine: GL_VENDOR: Mesa Project GL_RENDERER: Software Rasterizer GL_VERSION: 1.4 (2.1 Mesa 7.3-devel) Traceback (most recent call last): File /usr/lib/python2.5/site-packages/pymol/__init__.py, line 400, in launch_gui __import__(self.invocation.options.gui) File /usr/lib/python2.5/site-packages/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /usr/lib/python2.5/site-packages/pmg_tk/PMGApp.py, line 28, in module from Tkinter import * File /usr/lib/python2.5/lib-tk/Tkinter.py, line 38, in module import _tkinter # If this fails your Python may not be configured for Tk ImportError: /usr/local/chimera/lib/libtk8.5.so: cannot restore segment prot after reloc: Permission denied Detected 2 CPU cores. Enabled multithreaded rendering. Kindly suggest me what is going wrong, Thanks in advance, Bala
[PyMOL] gui/viewer position
hello, is it possible to define the gui and viewer positions on startup separately? thanks, marc
[PyMOL] gui-programming
Hi folks, I figured out how to preselect a Radiobutton in a Tkinter-GUI. One ought to use .select() instead of .set(). But now I've come up with another problem: How do I get the actual value of that Radiobutton? For some reason .get() is returning 0 all the times. from Tkinter import * radio = Tk() radiovar = IntVar() Yes = Radiobutton(radio, text='Yes', value =1, variable = radiovar) Yes.pack(side = LEFT) Yes.select() No = Radiobutton(radio, text='No', value =2, variable = radiovar) No.pack(side=LEFT) Although .get() does not work, displaying the actual value of radiovar as a dynamic label on the GUI works very well: Label(radio, textvariable=radiovar).pack(side = RIGHT) How do I get the actual value of that Radiobutton? In case .get() doesn't work at all, is there a way of reading out the textvariable of the Label? I would appreciate any help. Regards, Martin -- DSL-Aktion wegen großer Nachfrage bis 28.2.2006 verlängert: GMX DSL-Flatrate 1 Jahr kostenlos* http://www.gmx.net/de/go/dsl
Re: [PyMOL] gui-programming
radiovar.get() seems to work fine for me with the code you provided. You mention .get() but you never say radiovar.get(), so is that what you meant? Also, radiovar.set(2) works as well for changing the selection. - Charlie On 2/13/06, Martin Weisel martin.wei...@gmx.de wrote: Hi folks, I figured out how to preselect a Radiobutton in a Tkinter-GUI. One ought to use .select() instead of .set(). But now I've come up with another problem: How do I get the actual value of that Radiobutton? For some reason .get() is returning 0 all the times. from Tkinter import * radio = Tk() radiovar = IntVar() Yes = Radiobutton(radio, text='Yes', value =1, variable = radiovar) Yes.pack(side = LEFT) Yes.select() No = Radiobutton(radio, text='No', value =2, variable = radiovar) No.pack(side=LEFT) Although .get() does not work, displaying the actual value of radiovar as a dynamic label on the GUI works very well: Label(radio, textvariable=radiovar).pack(side = RIGHT) How do I get the actual value of that Radiobutton? In case .get() doesn't work at all, is there a way of reading out the textvariable of the Label? I would appreciate any help. Regards, Martin -- DSL-Aktion wegen großer Nachfrage bis 28.2.2006 verlängert: GMX DSL-Flatrate 1 Jahr kostenlos* http://www.gmx.net/de/go/dsl --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] gui-programming
Hi everybody. I'm currently trying to create a pop-up GUI with Radiobuttons (e.g. checkboxes). I don't know why initial highlighting of a specific Checkbox won't work. Attribute .set() fails at this point (see below), although the GUI looks nice. from Tkinter import * root = Tk() def radio1(): global tmp tmp = IntVar() for i in range(10): rad = Radiobutton(root, text = str(i), value = i , variable = tmp) rad.pack(side = LEFT) tmp.set(5) radio1() root.mainloop() Any help would be appreciated. Regards, Martin -- Telefonieren Sie schon oder sparen Sie noch? NEU: GMX Phone_Flat http://www.gmx.net/de/go/telefonie
[PyMOL] GUI
Hi Warren, Why can't we have little check marks in the main menu that indicate the current setting? For example, SettingRenderingAntialias gets a check, but selecting SettingRenderingShadowsNone doesn't give a check (as do any of the other rendering options). Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
RE: [PyMOL] GUI
Hi- I'd second this; my brain doesn't do well keeping track of whether I'm, for example, in maximum or reasonable performance mode. David - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Mark A Saper Sent: Friday, January 20, 2006 3:01 PM To: Pymol Subject: [PyMOL] GUI Hi Warren, Why can't we have little check marks in the main menu that indicate the current setting? For example, SettingRenderingAntialias gets a check, but selecting SettingRenderingShadowsNone doesn't give a check (as do any of the other rendering options). Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] GUI output font size too small
Hi Bjorn, Unfortunately, this isn't configurable at runtime yet. We'll need to do something about this... For now, you'll need to directly edit the code in modules/pmg_tk/skins/normal/__init__.py look for self.font and text.configure. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Björn Kauppi Sent: Thursday, January 19, 2006 5:02 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] GUI output font size too small Hi, How do I control the GUI output window font size? It is too small for my eyes on a 1600x1200 screen. I can change it manually to 12 points in the GUI window Setting/Output size, but I can not find a command to do it for my .pymolrc! Preferably to more than 12 points as well... I use 0.99beta33 on Linux and windows. Thanks, Björn Kauppi ** * This e-mail may contain confidential information proprietary to Karo Bio AB and is meant for the intended addressee(s) only. Any unauthorized review, use, disclosure or distribution is prohibited. If you have received this message in error, please advise the sender and delete the e-mail and any attachments from your files. Thank you! ** * --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=kkid3432bid#0486dat1642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] GUI problem on Win2000
Hello everybody
At home, I run pymol on Debian/Linux without any problems. However, at
university, we only have windows machines. So I downloaded and installed
Python2.2.1, ActiveTCL 8.3.4.3 and, of course, Pymol 0.82.
So far, I can run (and use) pymol giving commands in the OpenGL window, but
the GUI (which depends on Tcl/Tk) does not appear. The startup window gives
the following error message:
self.root = Tk()
File C:\PROGRA~1\PYTHON~1\Lib\lib-tk\Tkinter.py, line 1487, in __init__
self.tk = _tkinter.create(screenName, baseName, className)
TclError: Can't find a usable init.tcl in the following directories:
{C:\python21\tcl\tcl8.3 (guessing)} {} {C:\python21\tcl\tcl8.3
(guessing)}
C:/python21/tcl/tcl8.3 C:/PROGRA~1/PYTHON~1/lib/tcl8.3
c:/programme/lib/tcl8.3
c:/lib/tcl8.3 c:/lib/tcl8.3/library c:/library c:/../tcl8.3/library
../tcl8.3/
library
So, what can I do to help pymol finding init.tcl and display the GUI?
Thanks, joerg
PS.: Please CC: to me, as I'm not subscribed to this list.
--
Did you know that if you play a Windows 2000 cd backwards, you
will hear the voice of Satan?
That's nothing! If you play it forward, it'll install Windows 2000.
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