Re: [PyMOL] PyMOL 2.5 released
very good. When will this migrate to github.com/schrodinger/pymol-open-source.git? On 05/10/2021 12:27 PM, Jarrett Johnson wrote: Greetings, We are happy to announce the release of PyMOL 2.5. Download ready-to-use bundles from https://pymol.org/ or update your installation with "conda install -c schrodinger pymol". New features include: - Multiple-level undo for PyMOL actions (Incentive Only) - Curved cartoon cylindrical helices - Customizable keyboard shortcut menu - Improved isosurface generation - Nucleotides from the PDB can now be extended in builder (Incentive Only) - Improved MAE import (Incentive Only) - ...and more. Please check our release notes. Python 2 support has been removed. Python 2 to 3 converter tools including 2to3 may be useful if you need to update python scripts. Find the complete release notes at: https://pymol.org/d/media:new25 We welcome any feedback and bug reports. Cheers, - The PyMOL Team at Schr�dinger -- *Jarrett Johnson* | Senior Developer Schrodinger Logo <https://www.schrodinger.com/> ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1 ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Problem With Dynamic_Gromacs Plugin
I just downloaded, compiled and installed gromacs-2020 without any warnings or errors. However when I attempt opening the Dynamic_Gromacs 2.2.1 plugin I get the error: 'module' object has no attribute 'showerror' and everything stops. Now, the plugin has been working with the Debian Stretch default gromacs-2019.1. Further, with the gromacs 2020 installation gmx command executes correctly at the command line. I may be wrong, but, might this be a PyMOL error? Thanks in advance. -- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1 ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] Problem with autodock_plugin.py
uot;/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwNoteBook.py", line
153, in insert
Tkinter.Frame, self._hull), pageOptions)
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 465, in createcomponent
'Component name "%s" must not contain "_"' % componentName
: Component name "receptor.1acl_m" must
not contain "_"
The run.log and DME.dlg are also attached.
All very confusing.
Thanks in advance for your comments.
--
Stephen P. Molnar, Ph.D.
Consultant
www.molecular-modeling.net
(614)312-7528 (c)
Skype: smolnar1
Script started on Tue 05 Jun 2018 09:12:18 AM EDT
]0;comp@AbNormal: ~/Apps/Models/1ACL/PyMOL_Test[01;32mcomp@AbNormal[00m:[01;34m~/Apps/Models/1ACL/PyMOL_Test[00m$ /home/comp/Apps/PyMOL/pymol
PyMOL(TM) Molecular Graphics System, Version 2.2.0a0.
Copyright (c) Schrodinger, LLC.
All Rights Reserved.
Created by Warren L. DeLano, 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 " for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Detected OpenGL version 3.0. Shaders available.
Detected GLSL version 1.30.
OpenGL graphics engine:
GL_VENDOR: nouveau
GL_RENDERER: Gallium 0.4 on NVD9
GL_VERSION: 3.0 Mesa 13.0.6
Detected blacklisted graphics driver. Disabling shaders.
Detected 8 CPU cores. Enabled multithreaded rendering.
Gtk-[1;32mMessage[0m: GtkDialog mapped without a transient parent. This is discouraged.
HEADERHYDROLASE(CARBOXYLIC ESTERASE) 18-AUG-93 1ACL
TITLE QUATERNARY LIGAND BINDING TO AROMATIC RESIDUES IN THE ACTIVE-SITE
TITLE2 GORGE OF ACETYLCHOLINESTERASE
COMPNDMOL_ID: 1;
COMPND 2 MOLECULE: ACETYLCHOLINESTERASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.1.1.7;
COMPND 5 ENGINEERED: YES
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
CmdLoad: PDB-string loaded into object "1acl_m", state 1.
CmdLoad: PDB-string loaded into object "DME", state 1.
/home/comp/Apps/Models/1ACL/PyMOL_Test
/home/comp/Apps/Models/1ACL/PyMOL_Test/receptor.1acl_m.pdb
Exception in thread Thread-3:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 255, in run
self.page.insert('end', "%s" % line)
File "", line 1, in insert
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 3113, in insert
self.tk.call((self._w, 'insert', index, chars) + args)
RuntimeError: main thread is not in main loop
/home/comp/Apps/Autodock/autodock4: WARNING: Using autodock4.0 unbound extended model in autodock4.2!
Exception in thread Thread-5:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 255, in run
self.page.insert('end', "%s" % line)
File "", line 1, in insert
File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 3113, in insert
self.tk.call((self._w, 'insert', index, chars) + args)
RuntimeError: main thread is not in main loop
Exception in Tk callback
Function: > (type: )
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 2459, in load_ligand_file
self.load_pdbqt(filename)
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 2513, in load_pdbqt
lst = self.fileopen(filename, 'r').readlines()
: 'NoneType' object has no attribute 'readlines'
Gtk-[1;32mMessage[0m: GtkDialog mapped without a transient parent. This is discouraged.
Exception in Tk callback
Function: > (type: )
Args: ()
Traceback (innermost last):
File "/usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__
return apply(self.func, args)
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 2459, in load_ligand_file
self.load_pdbqt(filename)
File "/home/comp/Apps/PyMOL/modules/pmg_tk/startup/autodock_plugin.py", line 2540, in load_pdbqt
self.update_combo(name)
File &quo
[PyMOL] Optimize Geometry {rpblem
I have a bit of a strange problem. I have evaluated a number of Linux distributions in a VMware Player environment on my 64 bit laptop. I compile PyMol using the attached protocol. The OS is BioLinux v-8.0.5 with Avogadro Version 1.1.1 Library Version 1.1.1 Open Babel Version 2.3.2 Qt Version 4.8.6 The problem involves the Extensions/Optimize Geometry feature with cyclohexane as the test molecule. Cyclohexane as built is a planar molecule, but when I optimize the geometry it remains in a planar conformation. However in some of my test systems the geometry is returned as the chair isomer, which, of course, is correct! I will make the wild assumption (yes, I know how the word can be broken down) that there is a missing library. Which one might it be? Is any other information needed in order to address this rather nagging problem? Thanks in advance. -- Stephen P. Molnar, Ph.D.Life is a fuzzy set www.FoundationForChemistry.com Stochastic and multivariate (614)312-7528 (c) Skype: smolnar1 sudo apt-get install subversion build-essential python-dev python-pmw libglew-dev freeglut3-dev libpng-dev libfreetype6-dev libxml2-dev cd /tmp svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol cd pymol prefix=/home/comp/Apps/pymol modules=$prefix/modules export CPPFLAGS=-std=c++11 python setup.py build install \ --home=$prefix \ --install-lib=$modules \ --install-scripts=$prefix -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/___ 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] Caver 3.0 pugin
On 11/17/2013 03:02 PM, James Starlight wrote: Hi Stephen, you should try lattest CAVER which could be downloaded from http://www.caver.cz before installing it via Pymol plugin menu, you should to open caver-3.0-1.py http://caver-3.0-1.py and find here CAVER3_LOCATION = directory/where/caver3/is/located and modify this on your path providing it to the jar file directly ( in this version there is no jar path in pymol plugin itself). Does anyone use it for the analysis of the ligand sites? I've test it with the GPCR and found 3 possible pathways. I'n not sure how It have been clustered but now I'n looking for the method for the steered MD along caver-predicted pathes James 2013/11/17 Stephen P. Molnar s.mol...@sbcglobal.net mailto:s.mol...@sbcglobal.net I would be interested in just how the problem has been solved! I just installed caver v-2.1.2 in the 64 bit Debian Testing with PyMOL v-1.6.0.0 compiled from the latest svn and functioning perfectly on my system. Carver installed from the PyMOL wicki via the PyMOL Plugin Manager without any complaints. Yet when I try to use the plugin I get: ERROR: Directory incorrectly specified -plugin.jar not found, check directory/where/jar/with/plugin/is/locate/Carver2_1.jar Both Carver2_1_2.py and Carver2_1_2.pyc are in the startup subdirectory. Also other plugins are working without complaint. This is exactly the way the plug was working the last time that I attempted its installation and use. On 11/15/2013 03:14 PM, James Starlight wrote: This issue have been solved. Caver works fine. Does anyone tried to include path information obtained by caver to the NAMD steered md simulation? I'm looking for the protocol for guiding namd forces along the direction obtaned from CAVER. James 2013/11/15 James Starlight jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com Dear Pymol Users! In the latest 3.0 releases of the CAVER plugin lack the source path for the caver.jar launch file. Could you tell me how I could define this path manually from pymol shell? I've try to make calculations with thus plugin having Caver 3.0 dir in the work folder but obtained error that /where/caver3 not found Thanks for help James -- DreamFactory - Open Source REST JSON Services for HTML5 Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk ___ 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 -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com http://www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -- DreamFactory - Open Source REST JSON Services for HTML5 Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk ___ 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 Got it! Many thanks. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -- DreamFactory - Open Source REST JSON Services for HTML5 Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo
Re: [PyMOL] Caver 3.0 pugin
I would be interested in just how the problem has been solved! I just installed caver v-2.1.2 in the 64 bit Debian Testing with PyMOL v-1.6.0.0 compiled from the latest svn and functioning perfectly on my system. Carver installed from the PyMOL wicki via the PyMOL Plugin Manager without any complaints. Yet when I try to use the plugin I get: ERROR: Directory incorrectly specified -plugin.jar not found, check directory/where/jar/with/plugin/is/locate/Carver2_1.jar Both Carver2_1_2.py and Carver2_1_2.pyc are in the startup subdirectory. Also other plugins are working without complaint. This is exactly the way the plug was working the last time that I attempted its installation and use. On 11/15/2013 03:14 PM, James Starlight wrote: This issue have been solved. Caver works fine. Does anyone tried to include path information obtained by caver to the NAMD steered md simulation? I'm looking for the protocol for guiding namd forces along the direction obtaned from CAVER. James 2013/11/15 James Starlight jmsstarli...@gmail.com mailto:jmsstarli...@gmail.com Dear Pymol Users! In the latest 3.0 releases of the CAVER plugin lack the source path for the caver.jar launch file. Could you tell me how I could define this path manually from pymol shell? I've try to make calculations with thus plugin having Caver 3.0 dir in the work folder but obtained error that /where/caver3 not found Thanks for help James -- DreamFactory - Open Source REST JSON Services for HTML5 Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk ___ 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 -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -- DreamFactory - Open Source REST JSON Services for HTML5 Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471iu=/4140/ostg.clktrk___ 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] Pymol v-1.6.0 in Debian Testing Jessie
I have Debian Testing/Jessie installed in a VMware Player v-6.0 on my 64 bit Laptop as a testbed before installing apps on my native Linux production computer. I have installed the Debian package from the Jessie repository, but it crashes when I try to open it. The run log is attached. If anyone has encountered this problem I would appreciate some pointers towards a solution. Thinks in advance. /usr/bin/pymol PyMOL(TM) Molecular Graphics System, Version 1.6.0.0. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, 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. Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: VMware, Inc. GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.2, 256 bits) GL_VERSION: 2.1 Mesa 9.1.6 Detected 4 CPU cores. Enabled multithreaded rendering. HEADERCOMPLEX (HYDROLASE/PEPTIDE) 01-AUG-96 1YTI TITLE SIV PROTEASE CRYSTALLIZED WITH PEPTIDE PRODUCT COMPNDMOL_ID: 1; COMPND 2 MOLECULE: SIV PROTEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SIV PROTEINASE; COMPND 5 EC: 3.4.23.16; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PEPTIDE PRODUCT; COMPND 10 CHAIN: I; COMPND 11 ENGINEERED: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. Symmetry: Found 8 symmetry operators. CmdLoad: /home/computation/1yti.pdb loaded as 1yti. LLVM ERROR: Cannot select: 0x2938f10: i32 = fneg 0x2926800 [ID=456] 0x2926800: i32 = extract_vector_elt 0x291df80, 0x28ba120 [ID=448] 0x291df80: v4i32 = extract_subvector 0x29441a0, 0x292d870 [ID=440] 0x29441a0: v8i32 = X86ISD::VBROADCAST 0x292ed80 [ID=437] 0x292ed80: i32,ch = load 0x288d3f0, 0x28ad660, 0x288d7f0LD4[%270] [ORD=703] [ID=436] 0x28ad660: i64 = add 0x28ad970, 0x2907e90 [ORD=701] [ID=435] 0x28ad970: i64,ch = load 0x288d3f0, 0x28ab950, 0x288d7f0LD8[%183] [ORD=700] [ID=431] 0x28ab950: i64,ch = CopyFromReg 0x281f190, 0x28acf60 [ORD=608] [ID=151] 0x28acf60: i64 = Register %vreg52 [ORD=608] [ID=34] 0x288d7f0: i64 = undef [ORD=535] [ID=18] 0x2907e90: i64 = Constant48 [ORD=629] [ID=38] 0x288d7f0: i64 = undef [ORD=535] [ID=18] 0x292d870: i64 = Constant4 [ID=86] 0x28ba120: i32 = Constant0 [ID=87] In function: fs34_variant0_partial pure virtual method called terminate called without an active exception Aborted computation@inga:~$ -- How ServiceNow helps IT people transform IT departments: 1. Consolidate legacy IT systems to a single system of record for IT 2. Standardize and globalize service processes across IT 3. Implement zero-touch automation to replace manual, redundant tasks http://pubads.g.doubleclick.net/gampad/clk?id=5127iu=/4140/ostg.clktrk___ 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 Compiling v 1.6.0.0 in 64 bit Debian Testing
I have just installed the 64 bit Debian Testing distribution in an Oracle VM on my laptop as a test bed. I successfully compiled v 1.6.0.0 in my 6 bit Debian Wheezy production OS. I didn't get any error messages from my laptop installation during the compilation process. However when run pymol only the viewer window opens! Here are the messages: computation@inga:~/Apps/pymol/bin$ ./pymol PyMOL(TM) Molecular Graphics System, Version 1.6.0.0. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, 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. Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.40. OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU OpenGL graphics engine: GL_VENDOR: Humper GL_RENDERER: Chromium GL_VERSION: 2.1 Chromium 1.9 Traceback (most recent call last): File /home/computation/Apps/pymol/lib/python/pymol/__init__.py, line 448, in launch_gui __import__(self.invocation.options.gui) File /home/computation/Apps/pymol/lib/python/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /home/computation/Apps/pymol/lib/python/pmg_tk/PMGApp.py, line 31, in module import Pmw ImportError: No module named Pmw Detected 4 CPU cores. Enabled multithreaded rendering. OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU Unfortunately, I don't have the faintest idea as to what is missing. Any assistance will be appreciated. Thanks in advance. -- Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for ChemistryStochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ 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] Problem Compiling v 1.6.0.0 in 64 bit Debian Testing
On Tue, 25 Jun 2013 09:47:19 -0400 Robert Campbell robert.campb...@queensu.ca wrote: Hi Stephen, On Tue, 2013-06-25 09:16 EDT, Stephen P. Molnar s.mol...@sbcglobal.net wrote: I have just installed the 64 bit Debian Testing distribution in an Oracle VM on my laptop as a test bed. I successfully compiled v 1.6.0.0 in my 6 bit Debian Wheezy production OS. I didn't get any error messages from my laptop installation during the compilation process. However when run pymol only the viewer window opens! Here are the messages: Traceback (most recent call last): File /home/computation/Apps/pymol/lib/python/pymol/__init__.py, line 448, in launch_gui __import__(self.invocation.options.gui) File /home/computation/Apps/pymol/lib/python/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /home/computation/Apps/pymol/lib/python/pmg_tk/PMGApp.py, line 31, in module import Pmw ImportError: No module named Pmw Detected 4 CPU cores. Enabled multithreaded rendering. OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU Unfortunately, I don't have the faintest idea as to what is missing. Any assistance will be appreciated. Thanks in advance. I would appear that you are just missing the python-pmw package on this machine, whereas it must have been present on your Wheezy version. Cheers, Rob Rob Thanks for the suggestion. You were quite correct. Although, when I check with Synaptic python-pmw was installed I reinstalled it and the compilation worked correctly this time. Many thanks Steve -- Stephen P. Molnar, Ph.D.Life is a fuzzy set Foundation for ChemistryStochastic and multivariate www.FoundationForChemistry.com (614)312-7528 (c) Skype: smolnar1 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ 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] Problems with Pymol v 1.6.0.0
Two minor, but annoying, problems with the new version in Debian 7.0 64 bit/ #1 The pull down menus in the graphics windows refuse to remain open when clicked, unless I left click and hold. Is this normal behavior? #2. Caver 2.1.2 will not save the location of the Directory with the plug-in .jar file. The work around is rather cumbersome. -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev___ 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] PyMOL 1.6 pre-release announcement
On Sun, 24 Mar 2013 11:02:08 +0100 Thomas Holder thomas.hol...@schrodinger.com wrote: Dear PyMOL users, The pre-release version of PyMOL 1.6 has been pushed to the open source repository on SourceForge. Besides several minor fixes and improvements, this version should complete the transition to shader-based rendering for all on-screen drawing. For non-integrated chipsets this typically means higher quality and quicker rendering. Please also note that the URL of the SVN repository changed due to an upgrade of the SourceForge website: svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol As always, we welcome bug reports and positive feedback. Cheers, - The PyMOL Team at Schrödinger I managed to download the source code. There were a lot of warnings during the compilation and I got the following error message: usr/include/python2.7 -c layer1/TypeFace.c -o build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math -funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error: ft2build.h: No such file or directory compilation terminated. I don't have the faintest idea as to what supplies ft2build.h and would appreciate a point in the correct direction. Thanks in advance. -- 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_mar ___ 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] PyMOL 1.6 pre-release announcement
On Mon, 25 Mar 2013 18:47:27 +0100 Michael Banck mba...@debian.org wrote: Hi Stephen, On Mon, Mar 25, 2013 at 01:33:16PM -0400, Stephen P. Molnar wrote: On Sun, 24 Mar 2013 11:02:08 +0100 Thomas Holder thomas.hol...@schrodinger.com wrote: The pre-release version of PyMOL 1.6 has been pushed to the open source repository on SourceForge. Besides several minor fixes and improvements, this version should complete the transition to shader-based rendering for all on-screen drawing. For non-integrated chipsets this typically means higher quality and quicker rendering. Please also note that the URL of the SVN repository changed due to an upgrade of the SourceForge website: svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol As always, we welcome bug reports and positive feedback. Cheers, - The PyMOL Team at Schrödinger I managed to download the source code. There were a lot of warnings during the compilation and I got the following error message: usr/include/python2.7 -c layer1/TypeFace.c -o build/temp.linux-x86_64-2.7/layer1/TypeFace.o -ffast-math -funroll-loops -O3 -fcommon layer1/TypeFace.c:25:22: fatal error: ft2build.h: No such file or directory compilation terminated. I don't have the faintest idea as to what supplies ft2build.h and would appreciate a point in the correct direction. It's shipped by the libfreetype development package. Michael -- 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_mar ___ 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 Many thanks, That solved the problem! v1.6.0 is now compiled and installed. -- 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_mar ___ 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 get pymol 1.4
Going to www.pymol.org, clicking on OpenSource and then sf.net/projects/pymol/develop followed by Download PyMOL Molecular Graphics System will download pumol-1.3r2-src.tar.bz2. I would like to know if, and when, 1.4 will be available for downloading. Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivriate http://www.FoundationForChemistry.com From: Michael Lerner [mailto:mgler...@gmail.com] Sent: Wednesday, March 23, 2011 2:22 PM To: li...@cowsandmilk.net Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to get pymol 1.4 In addition to David's excellent email, I would like to point out that Jason is extremely dedicated to the open-source future of PyMOL, so much so that I don't think a better PyMOL maintainer could have been chosen. I think that, for people who have been using/contributing to PyMOL for a long time, there's a natural inclination to say Oh no! A more commercial entity is now in charge! and assume that things are both worse than they are and likely to get even worse. I certainly had some of those thoughts myself, but I've talked with Jason many times (sometimes initiated by me and sometimes initiated by him) and I'm convinced that things are in excellent hands. Just as an example of how it's easy to assume the worst, there have been quite a few complaints about the way in which PyMOL is hosted on Sourceforge. People went to download the source and, instead of a source tarball, found a link to a text file. Outrage at the fact that the actual source had somehow been hidden was then expressed. First of all, that text file contained very clear instructions on how to actually download the source. Second, and this will likely come as a complete shock to the people who complained, the text file is EXACTLY the system that Warren put in place. You may want to read that again, because, as far as I know, nobody complained about the system when Warren was in charge, but many people lept to the conclusion that nefarious forces were at work when they saw the exact same system under Schrodinger. Third, and perhaps most important, Jason's reaction upon hearing these complaints was to add a source tarball to the Sourceforge download page. If you go to pymol.org and click on open source, you go directly to the Sourceforge page from which you can download that tarball. So, if anything, PyMOL's open-source nature is *more* accessible now. I would say the the creation of the Warren L. DeLano Memorial PyMOL Open-Source Fellowship also clearly demonstrates Schrodinger's commitment to both open source and the PyMOL community, although I should mention in the interest of full disclosure that I have the great honor of receiving the 2010-2011 fellowship. I'm sure there are several other examples like this, but the main thing I'd like to say is that Jason is very accessible (both via email and through this list) and extremely responsive. If you're worried about something, especially something as important as the continuing open-source nature of PyMOL, try sending a collegial email to the list. PyMOL's userbase is huge, and I'm sure that many other people have the same concern. I'm also sure that Jason (or someone else on the list) will give you a surprisingly good answer. Open-source code thrives on community and trust, and I've really seen no signs to indicate that those aren't still to be had in top-notch form with PyMOL. Cheers, -Michael On Wed, Mar 23, 2011 at 7:12 AM, li...@cowsandmilk.net wrote: a) you're mistaken, Warren's incentive builds had extra features. Also, Warren had announced pretty clear plans of adding more features to the incentive builds and not releasing them open source for several years b) if you've been following the list, Jason has stated that many of the 1.4 features are on their way to the open source repository. Sure, I am of the type that wishes all features were open source and that Jason did all development directly against a repository we could all see, but I think he's done a good job communicating the way development is happening to the list and schrodinger's model for the incentive builds seems to be hardly different from what Warren had started doing. -David On Mar 23, 2011, at 6:33 AM, Abhinav Verma abhinav1...@gmail.com wrote: And why would that be? I thought that pymol is open source and till Warren was there all updates were available in the open source domain and incentive builds were limited to windows executable and involving support!! On Wed, Mar 23, 2011 at 11:15 AM, Mark J van Raaij mjvanra...@cnb.csic.es wrote: Is the 1.4 version restricted to incentive downloads only?? Yes Thanks, -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security
Re: [PyMOL] How to get pymol 1.4
Thank you for your reply. I was too much in a hurry to write. I shall curb my impatience and wait for your announcement. Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivriate http://www.FoundationForChemistry.com -Original Message- From: Jason Vertrees [mailto:jason.vertr...@schrodinger.com] Sent: Wednesday, March 23, 2011 3:07 PM To: Stephen P Molnar Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to get pymol 1.4 Hi Stephen, I would like to know if, and when, 1.4 will be available for downloading. Yes, PyMOL v1.4 will be released to the open-source. I will prepare the v1.4 release file soon (hopefully less than two weeks' time). As Michael noted, it's nothing insidious: within hours of releasing the v1.4 to the incentive users, I had to get in a plane and fly to the west coast to present and support PyMOL. I'm at the crystallographic WCPCW meeting this week, and ACS next week. When I return home, I'll merge the volumes code and make the release file. I'll announce it when I finish and it's posted. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar ___ 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] Problem Compiling Pymol 1.2.x
On 11/20/2009 07:43 PM, Jason Vertrees wrote: Stephen, openSuse Linux does not come with Pmw installed by default. Please re-download and install Pmw. Let me know if it's something else. -- Jason Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Fri, Nov 20, 2009 at 4:54 PM, Justin Lecher j.lec...@fz-juelich.de wrote: Stephen P. Molnar wrote: Here's teh end of the log file that I recorded. I really don't have anyplace to which to upload the entire 125 kb log file. Hi Stephen, as Donnie already mentioned, we cannot help if we could not see the _complete_ build.log. From the part you past, it looks succesfull. So please try to provide us the log, in worst case compress it and attach it to your mail. What exactly is the output if you start it in a shell? Justin -- Justin Lecher Institute for Neuroscience and Biophysics ISB 3 - Institute for structural biochemistry Research Centre Juelich GmbH, 52425 Juelich,Germany phone: +49 2461 61 5385 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 Many thanks. That was the missing library. The compilation was completly successful. I still have a bit of a problem, however. When I attempt toinstall a new plugin I get an error message: Unable to write to the plugin directory. Perhaps you have insufficient privileges? I don't understand this as /home/computation/Applications/pymol/modules/pmg_tk/startup has rwx privileges, -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate http://www.FoundationForChemistry.com -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 Compiling Pymol 1.2.x
I had successfully compiled Plymol from the Subversion repository in OpenSuSE v103. Linux. I say successfully, because I have just upgraded my linux computer to OpenSuSE v11.2. Unfortunaltely, I have a bit of a problem compiling the source code in the new linux OS in that I can compile the PyMol Viewer but notthe Pcl/Tck GUI. Obviously there is something missing in the new compiler installation, but I don't have the faintest idea as to what it could be. I was wonderig if anyone else has encountered this problem and/or might have a possible solution? Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and multivariate http://www.FoundationForChemistry.com -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Problem Compiling Pymol 1.2.x
On 11/20/2009 02:16 PM, Donnie Berkholz wrote: On 13:38 Fri 20 Nov , Stephen P. Molnar wrote: I had successfully compiled Plymol from the Subversion repository in OpenSuSE v103. Linux. I say successfully, because I have just upgraded my linux computer to OpenSuSE v11.2. Unfortunaltely, I have a bit of a problem compiling the source code in the new linux OS in that I can compile the PyMol Viewer but notthe Pcl/Tck GUI. Obviously there is something missing in the new compiler installation, but I don't have the faintest idea as to what it could be. I was wonderig if anyone else has encountered this problem and/or might have a possible solution? Dear Stephen, Could you supply the complete error message you encountered, along with the final line of compilation? It's very difficult to make any suggestions without seeing exactly what happened. If it's unclear to you what to send, just upload the whole build log somewhere and post a link to it here. Here's teh end of the log file that I recorded. I really don't have anyplace to which to upload the entire 125 kb log file. running install running install_lib copying build/lib.linux-x86_64-2.6/pymol/_cmd.so - /usr/local/lib64/python2.6/site-packages/pymol copying build/lib.linux-x86_64-2.6/pymol/opengl/glu/_glu_num.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/glu copying build/lib.linux-x86_64-2.6/pymol/opengl/glu/_glu.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/glu copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/openglutil_num.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/gl copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/_opengl.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/gl copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/_opengl_num.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/gl copying build/lib.linux-x86_64-2.6/pymol/opengl/gl/openglutil.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/gl copying build/lib.linux-x86_64-2.6/pymol/opengl/glut/_glut.so - /usr/local/lib64/python2.6/site-packages/pymol/opengl/glut copying build/lib.linux-x86_64-2.6/chempy/champ/_champ.so - /usr/local/lib64/python2.6/site-packages/chempy/champ running install_egg_info Removing /usr/local/lib64/python2.6/site-packages/pymol-1.2.0-py2.6.egg-info Writing /usr/local/lib64/python2.6/site-packages/pymol-1.2.0-py2.6.egg-info After running: python setup.py install Please run, to complete the installation: python setup2.py install To uninstall PyMOL, run: python setup2.py uninstall [1m[31mabnormal:/sda1/src/pymol # (B[mpython setup2.py install Installing into /usr/local/lib64/python2.6/site-packages ... Created ./pymol which can be used to launch PyMOL. You may wish to copy this file into a standard location such as /usr/bin or /usr/local/bin. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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
