Re: [PyMOL] Electrostatic potential surface
The problem with pdb2pqr have been solved :) Another question which I have is the calculation of the potential maps from the ensemble of the conformers (for example I want to compare potential distribution from the ensemble of the x-ray structures of one protein which were solved in different condition). In the visualization tab I found that APBS-2 can align maps. But what is the most suitable way to provide such ensemble for the calculations ? Should it be in NMR-like format or each conformer should be loaded by means of poadDir for instance ? How I can calculate maps from all conformers at once ? James 2013/3/28 James Starlight jmsstarli...@gmail.com by the way have someone had problems with the pdb2pqr usage with APBS in pymol? I've tried to install pdb2pqr from source as well as via packages then I've add usr/bin/pdb2pqr to the APBs plugin window and when I've started APBS I obtained error like Error: 5 type 'exceptions.UnboundLocalError' Exception in Tk callback Function: function lambda at 0x333fcf8 (type: type 'function') 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 /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 153, in lambda command=lambda self=self, name=name: self._doCommand(name)) File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 132, in _doCommand return command(name) File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1036, in execute good = self.generatePqrFile() File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1007, in generatePqrFile good = self._generatePdb2pqrPqrFile() File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1615, in _generatePdb2pqrPqrFile if retval != 0: type 'exceptions.UnboundLocalError': local variable 'retval' referenced before assignment If I launch pdb2pqr from the terminal I've obtained own@starlight ~/Desktop $ pdb2pqr Usage: pdb2pqr.py [options] PDB_PATH PQR_OUTPUT_PATH pdb2pqr.py: error: Incorrect number (0) of arguments! argv: ['/usr/share/pdb2pqr/pdb2pqr.py'], args: [] should I provide some addition paths to the bash? James 2013/3/27 James Starlight jmsstarli...@gmail.com: As I understood the APBs plugin which already exist in PyMol is the very efficient device for electrostatic potential calculations. 2 questions have been arisen: 1- How I could change cut-off distances for the electrostatic? E.g I'd like to consider only interactions within 5 A between any charged groups. 2- What advantages has the usage of pdb2pqr plugin? Also in the pdb2pqr tools options I've found some options for force fields. As I know Poisson-Boltzmann equation on which APBS is based doesnt need any force fields (charge calculation from ab initio principles). Why force fields used here ? 3- IS there other plugins for the electrostatic surface calculation with (1) possibility to change cut-offs and (2) charge assignment from the force fields or ab initio calculations ? Thanks for help, James 2013/3/27 Mike Marchywka marchy...@hotmail.com: I have a similar requirement, taking density and potential dstriutbutions from jdftx which are written as plain binarry doubles. I use a script and some code to create an xplor file which seems to work but I have to adjust the position and scale to let it overlay the ion positions that I read from an xyz file. AFAICT xplor is about the only easy format that pymol takes but I was debating about trying to find others. i think I dug through my older version of pymol, went to the effort of changing it all to c++/extern c and then dropped it. The xplor approch seems to work well enough for now. Is there an easier way? Thanks. Date: Wed, 27 Mar 2013 13:41:24 +0400 From: jmsstarli...@gmail.com To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Electrostatic potential surface Dear PyMol users! I wounder to know about built-in PyMol option for electrostatic potential visualisation. For example I have pdb coordinates of my protein as well as its electrostatic potential distribution (calculated by another software). Using MolMol with both of that files I can visualize the electrostatic potential surface by means of PaintSurface option. Can I do the same with the PyMOl? Thanks for help, James -- Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13.
Re: [PyMOL] Electrostatic potential surface
I have a similar requirement, taking density and potential dstriutbutions from jdftx which are written as plain binarry doubles. I use a script and some code to create an xplor file which seems to work but I have to adjust the position and scale to let it overlay the ion positions that I read from an xyz file. AFAICT xplor is about the only easy format that pymol takes but I was debating about trying to find others. i think I dug through my older version of pymol, went to the effort of changing it all to c++/extern c and then dropped it. The xplor approch seems to work well enough for now. Is there an easier way? Thanks. Date: Wed, 27 Mar 2013 13:41:24 +0400 From: jmsstarli...@gmail.com To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Electrostatic potential surface Dear PyMol users! I wounder to know about built-in PyMol option for electrostatic potential visualisation. For example I have pdb coordinates of my protein as well as its electrostatic potential distribution (calculated by another software). Using MolMol with both of that files I can visualize the electrostatic potential surface by means of PaintSurface option. Can I do the same with the PyMOl? Thanks for help, James -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ 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 -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ 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] Electrostatic potential surface
As I understood the APBs plugin which already exist in PyMol is the very efficient device for electrostatic potential calculations. 2 questions have been arisen: 1- How I could change cut-off distances for the electrostatic? E.g I'd like to consider only interactions within 5 A between any charged groups. 2- What advantages has the usage of pdb2pqr plugin? Also in the pdb2pqr tools options I've found some options for force fields. As I know Poisson-Boltzmann equation on which APBS is based doesnt need any force fields (charge calculation from ab initio principles). Why force fields used here ? 3- IS there other plugins for the electrostatic surface calculation with (1) possibility to change cut-offs and (2) charge assignment from the force fields or ab initio calculations ? Thanks for help, James 2013/3/27 Mike Marchywka marchy...@hotmail.com: I have a similar requirement, taking density and potential dstriutbutions from jdftx which are written as plain binarry doubles. I use a script and some code to create an xplor file which seems to work but I have to adjust the position and scale to let it overlay the ion positions that I read from an xyz file. AFAICT xplor is about the only easy format that pymol takes but I was debating about trying to find others. i think I dug through my older version of pymol, went to the effort of changing it all to c++/extern c and then dropped it. The xplor approch seems to work well enough for now. Is there an easier way? Thanks. Date: Wed, 27 Mar 2013 13:41:24 +0400 From: jmsstarli...@gmail.com To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Electrostatic potential surface Dear PyMol users! I wounder to know about built-in PyMol option for electrostatic potential visualisation. For example I have pdb coordinates of my protein as well as its electrostatic potential distribution (calculated by another software). Using MolMol with both of that files I can visualize the electrostatic potential surface by means of PaintSurface option. Can I do the same with the PyMOl? Thanks for help, James -- Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ 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 -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ 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] Electrostatic potential surface
by the way have someone had problems with the pdb2pqr usage with APBS in pymol? I've tried to install pdb2pqr from source as well as via packages then I've add usr/bin/pdb2pqr to the APBs plugin window and when I've started APBS I obtained error like Error: 5 type 'exceptions.UnboundLocalError' Exception in Tk callback Function: function lambda at 0x333fcf8 (type: type 'function') 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 /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 153, in lambda command=lambda self=self, name=name: self._doCommand(name)) File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 132, in _doCommand return command(name) File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1036, in execute good = self.generatePqrFile() File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1007, in generatePqrFile good = self._generatePdb2pqrPqrFile() File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 1615, in _generatePdb2pqrPqrFile if retval != 0: type 'exceptions.UnboundLocalError': local variable 'retval' referenced before assignment If I launch pdb2pqr from the terminal I've obtained own@starlight ~/Desktop $ pdb2pqr Usage: pdb2pqr.py [options] PDB_PATH PQR_OUTPUT_PATH pdb2pqr.py: error: Incorrect number (0) of arguments! argv: ['/usr/share/pdb2pqr/pdb2pqr.py'], args: [] should I provide some addition paths to the bash? James 2013/3/27 James Starlight jmsstarli...@gmail.com: As I understood the APBs plugin which already exist in PyMol is the very efficient device for electrostatic potential calculations. 2 questions have been arisen: 1- How I could change cut-off distances for the electrostatic? E.g I'd like to consider only interactions within 5 A between any charged groups. 2- What advantages has the usage of pdb2pqr plugin? Also in the pdb2pqr tools options I've found some options for force fields. As I know Poisson-Boltzmann equation on which APBS is based doesnt need any force fields (charge calculation from ab initio principles). Why force fields used here ? 3- IS there other plugins for the electrostatic surface calculation with (1) possibility to change cut-offs and (2) charge assignment from the force fields or ab initio calculations ? Thanks for help, James 2013/3/27 Mike Marchywka marchy...@hotmail.com: I have a similar requirement, taking density and potential dstriutbutions from jdftx which are written as plain binarry doubles. I use a script and some code to create an xplor file which seems to work but I have to adjust the position and scale to let it overlay the ion positions that I read from an xyz file. AFAICT xplor is about the only easy format that pymol takes but I was debating about trying to find others. i think I dug through my older version of pymol, went to the effort of changing it all to c++/extern c and then dropped it. The xplor approch seems to work well enough for now. Is there an easier way? Thanks. Date: Wed, 27 Mar 2013 13:41:24 +0400 From: jmsstarli...@gmail.com To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Electrostatic potential surface Dear PyMol users! I wounder to know about built-in PyMol option for electrostatic potential visualisation. For example I have pdb coordinates of my protein as well as its electrostatic potential distribution (calculated by another software). Using MolMol with both of that files I can visualize the electrostatic potential surface by means of PaintSurface option. Can I do the same with the PyMOl? Thanks for help, James -- Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ 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 -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page:
