[PyMOL] More on Plugins
Hello, Since it is plugin season, I thought of contributing too. I have a plugin which is very specific to my research needs in structure based drug design. It marries the PyMOL interface with other command line software packages, such as DivCon and AMBER. Both these packages can be obtained from other sources. AMBER is a popular simulation package from UCSF. DivCon was developed at the Merz research group at Penn State and can be obtained from http://www.quantumbioinc.com I did not write this with the aim to distribute it but just as a way to learn Python and PyMOL. But my colleagues who have used it, describe it as useful. So, PyMOL users who have access to these programs might find it useful too. In addition to the features that use the above programs, there are other features not dependent on any external programs and could be helpful during visualization and analysis of biomolecular structures. Anyway, a short description of the plugin can be found at the following location from where it can be downloaded too: http://www.personal.psu.edu/kxr205/research/divscore.html The introduction to the plugin in the above webpage is pretty ambitious and was written when the realization that a PhD has to be finished had not sunk in. But the features that have been described will all work once the programs are installed correctly. The installation is straightforward and follows the pymol plugin philosophy. If anybody is interested and has problems installing it then please e-mail me. As for platform dependence -- Since it uses external programs such as AMBER and DivCon, they need to be compiled for the specific platform. I have tested it out on RedHat Linux and it works fine. The features that do not need external programs (not too many of them yet) are platform independent. I just checked out the sequence viewer in 0.96 and its great. Kaushik -- Kaushik Raha Merz Research Group Penn State University On Wednesday, July 14, 2004, at 03:56 PM, Warren DeLano wrote: Charles, Simply awesome! It works great on Windows and Mac too... Folks, I think we've finally hit on a workable paradigm for extending PyMOL's capabilities via these lightweight, end-user-installable plugins. You have my full encouragement -- go crazy with this stuff! This grass-roots user-driven development is exactly what PyMOL was supposed to enable... To help the sharing process along, I've created a new plugins page on the SourceForge site and welcome your submissions. http://pymol.sf.net/plugins.html I can already see that we'll need a user-friendly "Install Plugin..." menu item in the next release that will automatically copy plugin files to the correct location. In the meantime, installation directions can be found on that page... Provided that plugins are released under a suitable (non-viral) open-source license, I don't see any reason why good ones couldn't become part of the standard PyMOL distribution, which would of course save users the trouble of having to download and install them. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Charles Moad Sent: Wednesday, July 14, 2004 11:32 AM To: Michael George Lerner Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Plug-in Menu Thanks for the info. Using your APBS as an example I made a very simple remote pdb loader. You can check it out at "http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/"; or download it directly from "http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/remote_pdb_load.py";. It is inspired from chimera's remote pdb loading feature. Thanks again, - Charlie Michael George Lerner wrote: Hi, There's some example code in pymol/modules/pmg_tk/startup/__init__.py. You can see how it works by copying it (uncommented) into a new file and placing that file in pymol/modules/pmg_tk/startup. You'll see the new plugins the next time you start PyMOL. I have a larger plugin that I've written .. I'll be sending out an announcement about it later today. -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Wed, 14 Jul 2004, Charles Moad wrote: I am interested in developing some simple plugins for the new release, and I was wondering if there was a document or api specifying how to go about this. As the subject says, for example, how do you add a plugin entry to the new menu bar list. Thanks, Charles Moad Scientific Data Analysis Lab Indiana University --- This SF.Net em
RE: [PyMOL] Plug-in Menu
Charles, Simply awesome! It works great on Windows and Mac too... Folks, I think we've finally hit on a workable paradigm for extending PyMOL's capabilities via these lightweight, end-user-installable plugins. You have my full encouragement -- go crazy with this stuff! This grass-roots user-driven development is exactly what PyMOL was supposed to enable... To help the sharing process along, I've created a new plugins page on the SourceForge site and welcome your submissions. http://pymol.sf.net/plugins.html I can already see that we'll need a user-friendly "Install Plugin..." menu item in the next release that will automatically copy plugin files to the correct location. In the meantime, installation directions can be found on that page... Provided that plugins are released under a suitable (non-viral) open-source license, I don't see any reason why good ones couldn't become part of the standard PyMOL distribution, which would of course save users the trouble of having to download and install them. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Charles Moad > Sent: Wednesday, July 14, 2004 11:32 AM > To: Michael George Lerner > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Plug-in Menu > > Thanks for the info. Using your APBS as an example I > made a very simple remote pdb loader. You can check it out > at "http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/"; or > download it directly from > "http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/remote_pdb_load.py";. > > It is inspired from chimera's remote pdb loading feature. > > Thanks again, > - Charlie > > Michael George Lerner wrote: > > Hi, > > > > There's some example code in > pymol/modules/pmg_tk/startup/__init__.py. > > You can see how it works by copying it (uncommented) into a > new file > > and placing that file in pymol/modules/pmg_tk/startup. > You'll see the > > new plugins the next time you start PyMOL. I have a larger plugin > > that I've written .. I'll be sending out an announcement > about it later today. > > > > -michael > > > > -- > > This isn't a democracy;|_ |Michael Lerner > > it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan > > -Torrence, Bring It On| - against HTML email X | Biophysics > >| / \ | mler...@umich > > > > On Wed, 14 Jul 2004, Charles Moad wrote: > > > > > >>I am interested in developing some simple plugins for the new > >>release, and I was wondering if there was a document or api > specifying > >>how to go about this. As the subject says, for example, how do you > >>add a plugin entry to the new menu bar list. > >> > >>Thanks, > >> > >>Charles Moad > >>Scientific Data Analysis Lab > >>Indiana University > >> > >> > >>--- > >>This SF.Net email sponsored by Black Hat Briefings & Training. > >>Attend Black Hat Briefings & Training, Las Vegas July 24-29 > - digital > >>self defense, top technical experts, no vendor pitches, unmatched > >>networking opportunities. Visit www.blackhat.com > >>___ > >>PyMOL-users mailing list > >>PyMOL-users@lists.sourceforge.net > >>https://lists.sourceforge.net/lists/listinfo/pymol-users > >> > > > > > > > > --- > > This SF.Net email sponsored by Black Hat Briefings & Training. > > Attend Black Hat Briefings & Training, Las Vegas July 24-29 > - digital > > self defense, top technical experts, no vendor pitches, unmatched > > networking opportunities. Visit www.blackhat.com > > ___ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > --- > This SF.Net email is sponsored by BEA Weblogic Workshop FREE > Java Enterprise J2EE developer tools! > Get your free copy of BEA WebLogic Workshop 8.1 today. > http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
Re: [PyMOL] Plug-in Menu
Thanks for the info. Using your APBS as an example I made a very simple remote pdb loader. You can check it out at "http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/"; or download it directly from "http://euclid.uits.iupui.edu/~cmoad/pymolPlugins/remote_pdb_load.py";. It is inspired from chimera's remote pdb loading feature. Thanks again, - Charlie Michael George Lerner wrote: Hi, There's some example code in pymol/modules/pmg_tk/startup/__init__.py. You can see how it works by copying it (uncommented) into a new file and placing that file in pymol/modules/pmg_tk/startup. You'll see the new plugins the next time you start PyMOL. I have a larger plugin that I've written .. I'll be sending out an announcement about it later today. -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Wed, 14 Jul 2004, Charles Moad wrote: I am interested in developing some simple plugins for the new release, and I was wondering if there was a document or api specifying how to go about this. As the subject says, for example, how do you add a plugin entry to the new menu bar list. Thanks, Charles Moad Scientific Data Analysis Lab Indiana University --- This SF.Net email sponsored by Black Hat Briefings & Training. Attend Black Hat Briefings & Training, Las Vegas July 24-29 - digital self defense, top technical experts, no vendor pitches, unmatched networking opportunities. Visit www.blackhat.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users --- This SF.Net email sponsored by Black Hat Briefings & Training. Attend Black Hat Briefings & Training, Las Vegas July 24-29 - digital self defense, top technical experts, no vendor pitches, unmatched networking opportunities. Visit www.blackhat.com ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations
Hi all, APBS (http://agave.wustl.edu/apbs/) is a package that allows you to perform very fast, accurate electrostatics calculations. I've written a PyMOL plugin that allows you to run APBS and visualize the results very easily from within PyMOL (version 0.96 or higher). The plugin lets you configure all of the normal APBS parameters (whether you want the full nonlinear Poisson-Boltzmann equation or not, what the various dielectrics should be, ion concentrations, etc.). Also, the plugin comes with a visualization tab that can be used to aid in the visualization of any electrostatic potential. It's quite easy to install, thanks to PyMOL's new plugin system. Anyway, you can find the plugin on my webpage http://www.umich.edu/~mlerner/PyMOL/ or directly from http://www.umich.edu/~mlerner/PyMOL/apbs_tools.py drop it into pymol/modules/pmg_tk/startup/ and you're ready to go. Please let me know if you find this useful and/or have any questions or comments! -michael Here are the directions, taken from http://www.umich.edu/~mlerner/PyMOL/ This is a PyMOL plugin which lets you run APBS from within PyMOL. To install it, 1. Make sure you have PyMOL version 0.96 or higher. 2. Download a copy of apbs_tools.py and place it in pymol/modules/pmg_tk/startup/. Now, you'll see "APBS Tools..." under the Plugins menu. This plugin allows fairly complete configuration of APBS, but it's very easy to set up a standard electrostatic potential calculation: 1. Load your molecule into PyMOL 2. Load the plugin 3. Click on "Set grid" 4. Click on "Run APBS" 5. Use the plugin's "Visualization" tab to look at the results This will use PyMOL's new ability to assign AMBER charges and radii. If you wish to use your own externally-generated PQR file, you can set that up on the plugin's main page. The plugin should auto-detect the location of the APBS binary on your system, but you can set it manually under the "APBS Location" tab. My plugin can calculate appropriate grid lengths and spacings. It ensures that the grid spacing is 0.5A or finer. If you have APBS's psize.py installed and you wish to use it, you can set that up on the plugin's "APBS Location" tab. Finally, it's worth noting that the plugin's "Visualization" tab can be used for easy visualization of any electrostatic potential, not just things generated by APBS. -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
Re: [PyMOL] Plug-in Menu
Hi, There's some example code in pymol/modules/pmg_tk/startup/__init__.py. You can see how it works by copying it (uncommented) into a new file and placing that file in pymol/modules/pmg_tk/startup. You'll see the new plugins the next time you start PyMOL. I have a larger plugin that I've written .. I'll be sending out an announcement about it later today. -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich On Wed, 14 Jul 2004, Charles Moad wrote: > I am interested in developing some simple plugins for the new release, > and I was wondering if there was a document or api specifying how to go > about this. As the subject says, for example, how do you add a plugin > entry to the new menu bar list. > > Thanks, > > Charles Moad > Scientific Data Analysis Lab > Indiana University > > > --- > This SF.Net email sponsored by Black Hat Briefings & Training. > Attend Black Hat Briefings & Training, Las Vegas July 24-29 - > digital self defense, top technical experts, no vendor pitches, > unmatched networking opportunities. Visit www.blackhat.com > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
[PyMOL] Plug-in Menu
I am interested in developing some simple plugins for the new release, and I was wondering if there was a document or api specifying how to go about this. As the subject says, for example, how do you add a plugin entry to the new menu bar list. Thanks, Charles Moad Scientific Data Analysis Lab Indiana University
