Re: [PyMOL] RMSD and Helices in a Protein
Hi Angelo, instead of calculating RMSD you could monitor pairwise helix angles over states. See attached script, it depends on the http://www.pymolwiki.org/index.php/AngleBetweenHelices script. Cheers, Thomas On Thu, Mar 10, 2011 at 12:05 AM, Angelo Rossi angelo.raymond.ro...@gmail.com wrote: Hello: I have a protein with several helices and believe only one of them (the one closest to that active center) moves significantly during a simulation. Can someone suggest a way to use pymol to highlight the movement of the helices in this protein. I want to select 20 structures from a trajectory, highlight each helix in the protein and hopefully it will show significant movement of this specific responsible for activity. Thank you for any help you can provide. Kind regards, Angelo monitorhelices.py Description: Binary data -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] plugin dependencies
Just another reminder: If the version of the external python and the python shipped with PyMOL are different enough on the user's computer, the package might still fail to work in PyMOL even if the user has installed the package using the external python and edited the PYTHONPATH. So, how about ship all the BioPython packages you need in your python code together with your plugin? Of course all dependencies should be included. On 03/10/2011 06:17 AM, rv...@libero.it wrote: Hello everyone, my plugin needs Biopython. I wish check the Biopython installation by try: from Bio import AlignIO # or similar except ImportError: .. prompt the user with a msg .. The problem is: what the msg to the user? Downloading and installing Biopython is not enough: If the user downloads and installs Biopython in the external python interpreter still Biopython continues to be unavailable for the internal python interpreter in pyMOL. Of course the user could edit the PYTHONPATH environment variable and so all the python interpreters can read Biopython but working with environment variables could be too difficult for a not experienced user. Is there a simpler way? Cheers, roberto -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 breaks printing \b
Hi all, I want to print some info during loading of my data so I've added some print's. I wanted to take advantage of printing the backspace character \b to go back and overwrite the previous value. Unfortunately, I've found out that the finish_launching() command breaks this. Here is a simple example: #!/usr/bin/env python2 # -*- coding: utf-8 -*- import sys, time import pymol #pymol.finish_launching() for n in xrange(100): print(%3d %%\b\b\b\b\b\b % n), sys.stdout.flush() time.sleep(0.05) This will print a percentage without newlines. Uncommenting the pymol.finish_launching() line will break this: the backspace character seems to be ignored completely. I cannot finish_launching() after my loop since the loop loads cgo objects, thus it needs pymol fully opened to do so. Is pymol overloading the print function? What's wrong here? Thanks! -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ 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 breaks printing \b
Hi Nicolas, I want to print some info during loading of my data so I've added some print's. I wanted to take advantage of printing the backspace character \b to go back and overwrite the previous value. Can you use the curses Python module (http://docs.python.org/library/curses.html) for this? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] plugin dependencies
Hi Roberto, This has always been a stumbling block for PyMOL. Either you compile from source and add any modules you want, or you use what we provide in the Incentive or Academic builds. In the past, to keep PyMOL light Warren always shipped a stripped Python version. Because of PyMOL's utility as a platform for scripting, I think it's better to increase the size a bit and add more modules that expands its basic functionality. As a note, the new PyMOL builds will be quite a bit larger because we're adding more useful Python modules and some other libraries to the default install. Along with Numpy, PIL and friends, we'll also be distributing BioPython. Cheers, -- Jason On Thu, Mar 10, 2011 at 12:17 AM, rv...@libero.it rv...@libero.it wrote: Hello everyone, my plugin needs Biopython. I wish check the Biopython installation by try: from Bio import AlignIO # or similar except ImportError: .. prompt the user with a msg .. The problem is: what the msg to the user? Downloading and installing Biopython is not enough: If the user downloads and installs Biopython in the external python interpreter still Biopython continues to be unavailable for the internal python interpreter in pyMOL. Of course the user could edit the PYTHONPATH environment variable and so all the python interpreters can read Biopython but working with environment variables could be too difficult for a not experienced user. Is there a simpler way? Cheers, roberto -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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] R: Re: plugin dependencies
Hi Hongbo, thanks for your reply. So, how about ship all the BioPython packages you need in your python code together with your plugin? Of course all dependencies should be included. Is not so simple. A library like Biopython can't be installed as a plugin. An installer (OS specific) program is needed: the official windows installer I checked doesn't allow the user to choose the folder (this way the interpreter) where to install. Installing manually is still tricky for a not experienced user. Cheers, roberto Messaggio originale Da: hongbo@biotec.tu-dresden.de Data: 10/03/2011 12.57 A: pymol-users@lists.sourceforge.net Ogg: Re: [PyMOL] plugin dependencies Just another reminder: If the version of the external python and the python shipped with PyMOL are different enough on the user's computer, the package might still fail to work in PyMOL even if the user has installed the package using the external python and edited the PYTHONPATH. So, how about ship all the BioPython packages you need in your python code together with your plugin? Of course all dependencies should be included. On 03/10/2011 06:17 AM, rv...@libero.it wrote: Hello everyone, my plugin needs Biopython. I wish check the Biopython installation by try: from Bio import AlignIO # or similar except ImportError: .. prompt the user with a msg .. The problem is: what the msg to the user? Downloading and installing Biopython is not enough: If the user downloads and installs Biopython in the external python interpreter still Biopython continues to be unavailable for the internal python interpreter in pyMOL. Of course the user could edit the PYTHONPATH environment variable and so all the python interpreters can read Biopython but working with environment variables could be too difficult for a not experienced user. Is there a simpler way? Cheers, roberto -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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] R: Re: plugin dependencies
Hi Jason, thanks for your reply. As a note, the new PyMOL builds will be quite a bit larger because we're adding more useful Python modules and some other libraries to the default install. Along with Numpy, PIL and friends, we'll also be distributing BioPython. This is a good news. Could you also keep in consideration to include a 'dependencie manager' in the Plugin menu? A function 'check the plugin' could check import statements for the plugin and prompt the user on ImportError. A fileDialog window could allow the user to choose the installation folder of the library (if any). The script could edit the PYTHONPATH environment variable adding the library. I will try to write a dependency manager specific for my plugin but maybe the best solution is to have a general manager for every plugin. Cheers, roberto Messaggio originale Da: jason.vertr...@schrodinger.com Data: 10/03/2011 21.07 A: rv...@libero.itrv...@libero.it Cc: pymol-users@lists.sourceforge.net Ogg: Re: [PyMOL] plugin dependencies Hi Roberto, This has always been a stumbling block for PyMOL. Either you compile from source and add any modules you want, or you use what we provide in the Incentive or Academic builds. In the past, to keep PyMOL light Warren always shipped a stripped Python version. Because of PyMOL's utility as a platform for scripting, I think it's better to increase the size a bit and add more modules that expands its basic functionality. As a note, the new PyMOL builds will be quite a bit larger because we're adding more useful Python modules and some other libraries to the default install. Along with Numpy, PIL and friends, we'll also be distributing BioPython. Cheers, -- Jason On Thu, Mar 10, 2011 at 12:17 AM, rv...@libero.it rv...@libero.it wrote: Hello everyone, my plugin needs Biopython. I wish check the Biopython installation by try: from Bio import AlignIO # or similar except ImportError: .. prompt the user with a msg .. The problem is: what the msg to the user? Downloading and installing Biopython is not enough: If the user downloads and installs Biopython in the external python interpreter still Biopython continues to be unavailable for the internal python interpreter in pyMOL. Of course the user could edit the PYTHONPATH environment variable and so all the python interpreters can read Biopython but working with environment variables could be too difficult for a not experienced user. Is there a simpler way? Cheers, roberto -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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] R: Re: plugin dependencies
I really like the fact that Jason will be including more libraries with PyMOL in the future. I once needed to distribute a library that depended on BioPython. It turned out that, in my case, I only cared about a few specific files from BioPython, so I was able to strip out the necessary functionality and just ship that with my plugin. I don't know exactly what you're doing, but that might be an option. Cheers, -Michael On Thu, Mar 10, 2011 at 9:25 PM, rv...@libero.it rv...@libero.it wrote: Hi Hongbo, thanks for your reply. So, how about ship all the BioPython packages you need in your python code together with your plugin? Of course all dependencies should be included. Is not so simple. A library like Biopython can't be installed as a plugin. An installer (OS specific) program is needed: the official windows installer I checked doesn't allow the user to choose the folder (this way the interpreter) where to install. Installing manually is still tricky for a not experienced user. Cheers, roberto Messaggio originale Da: hongbo@biotec.tu-dresden.de Data: 10/03/2011 12.57 A: pymol-users@lists.sourceforge.net Ogg: Re: [PyMOL] plugin dependencies Just another reminder: If the version of the external python and the python shipped with PyMOL are different enough on the user's computer, the package might still fail to work in PyMOL even if the user has installed the package using the external python and edited the PYTHONPATH. So, how about ship all the BioPython packages you need in your python code together with your plugin? Of course all dependencies should be included. On 03/10/2011 06:17 AM, rv...@libero.it wrote: Hello everyone, my plugin needs Biopython. I wish check the Biopython installation by try: from Bio import AlignIO # or similar except ImportError: .. prompt the user with a msg .. The problem is: what the msg to the user? Downloading and installing Biopython is not enough: If the user downloads and installs Biopython in the external python interpreter still Biopython continues to be unavailable for the internal python interpreter in pyMOL. Of course the user could edit the PYTHONPATH environment variable and so all the python interpreters can read Biopython but working with environment variables could be too difficult for a not experienced user. Is there a simpler way? Cheers, roberto -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives:
[PyMOL] R: Re: R: Re: plugin dependencies
Hi Michael, did you install each scattered file as a plugin?I am considering this option although looks quite tricky for disinstallation. If I don't fail the authors of Biopython allow this scattered use of their code (a citation of course is needed). Cheers, roberto Messaggio originale Da: mgler...@gmail.com Data: 11/03/2011 4.05 A: rv...@libero.itrv...@libero.it Cc: hongbo@biotec.tu-dresden.de, pymol-users@lists.sourceforge.net Ogg: Re: [PyMOL] R: Re: plugin dependencies I really like the fact that Jason will be including more libraries with PyMOL in the future. I once needed to distribute a library that depended on BioPython. It turned out that, in my case, I only cared about a few specific files from BioPython, so I was able to strip out the necessary functionality and just ship that with my plugin. I don't know exactly what you're doing, but that might be an option. Cheers, -Michael On Thu, Mar 10, 2011 at 9:25 PM, rv...@libero.it rv...@libero.it wrote: Hi Hongbo, thanks for your reply. So, how about ship all the BioPython packages you need in your python code together with your plugin? Of course all dependencies should be included. Is not so simple. A library like Biopython can't be installed as a plugin. An installer (OS specific) program is needed: the official windows installer I checked doesn't allow the user to choose the folder (this way the interpreter) where to install. Installing manually is still tricky for a not experienced user. Cheers, roberto Messaggio originale Da: hongbo@biotec.tu-dresden.de Data: 10/03/2011 12.57 A: pymol-users@lists.sourceforge.net Ogg: Re: [PyMOL] plugin dependencies Just another reminder: If the version of the external python and the python shipped with PyMOL are different enough on the user's computer, the package might still fail to work in PyMOL even if the user has installed the package using the external python and edited the PYTHONPATH. So, how about ship all the BioPython packages you need in your python code together with your plugin? Of course all dependencies should be included. On 03/10/2011 06:17 AM, rv...@libero.it wrote: Hello everyone, my plugin needs Biopython. I wish check the Biopython installation by try: from Bio import AlignIO # or similar except ImportError: .. prompt the user with a msg .. The problem is: what the msg to the user? Downloading and installing Biopython is not enough: If the user downloads and installs Biopython in the external python interpreter still Biopython continues to be unavailable for the internal python interpreter in pyMOL. Of course the user could edit the PYTHONPATH environment variable and so all the python interpreters can read Biopython but working with environment variables could be too difficult for a not experienced user. Is there a simpler way? Cheers, roberto -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852
