[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] PyMOL + APBS for easy, accurate electrostatics calculations
Hi all I've been trying to install apbs to use this new plugin, as I imagine a lot of people will want to. I run into a problem in the compilation which I wonder if anyone can help with. [I know this is not strictly a Pymol question but given the general interest perhaps I can be excused. There seems to be a glitch with the apbs-users list too - my help awaits moderation which I know can take days] Anyway, after installation of the prerequisite MALOC (rpm or compiled, makes no difference) I get the following when trying to configure for apbs compilation -- begin configuring for MALOC linkage checking for FETK_INCLUDE... yes checking for FETK_LIBRARY... yes checking maloc/maloc.h usability... yes checking maloc/maloc.h presence... yes checking for maloc/maloc.h... yes checking for maloc_link in -lmaloc... no configure: error: MALOC libraries or headers missing: exiting on error! I saw some messages about libraries during compilation of maloc. I don't known if they have anything to do with the apbs compilation problem but I added /usr/local/lib/i686-pc-linux to /etc/ld.so.conf and did a /sbin/ldconfig and it didn't help. Any advice much appreciated Daniel On Wed, 2004-07-14 at 16:37, Michael George Lerner wrote: > 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 > > > --- > 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 -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4414 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.
Re: [PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations
On Thursday 15 July 2004 13:30, Daniel Rigden wrote:
> -- begin configuring for MALOC linkage
> checking for FETK_INCLUDE... yes
> checking for FETK_LIBRARY... yes
> checking maloc/maloc.h usability... yes
> checking maloc/maloc.h presence... yes
> checking for maloc/maloc.h... yes
> checking for maloc_link in -lmaloc... no
> configure: error: MALOC libraries or headers missing: exiting on error!
>
> I saw some messages about libraries during compilation of maloc. I
> don't known if they have anything to do with the apbs compilation
> problem but I added /usr/local/lib/i686-pc-linux to /etc/ld.so.conf and
> did a /sbin/ldconfig and it didn't help.
I went through the following steps:
# unpack maloc tarball
cd maloc
./configure --prefix=/usr/local
make
make install
#This produces some error messages which
# I still have to look into
cd ..
# unpack apbs tarball
cd apbs-0.3.1
export LDFLAGS="-L/usr/local/lib/i686-pc-linux"
export FETK_INCLUDE=/usr/local/include
export FETK_LIBRARY=/usr/local/lib
./configure --prefix=/usr/local
make
make install
"make install" steps were done as root. My LDFLAGS were empty before I
started. If they are not, you may have to use
export LDFLAGS="${LDFLAGS} -L/usr/local/lib/i686-pc-linux"
instead.
Hope this helps,
--
Lieven Buts
Department of Ultrastructure
Vrije Universiteit Brussel
[PyMOL] Re: PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 | 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. Short feedback: I tried APBS before (when there was no plugin) but somehow ran out of steam converting input for APBS and converting output to Pymol. Now I tried the Redhat-enabled rpms on SuSE 9.1 (you need to install maloc.rpms from the maloc-site and do a "rpm -Uhv --nodeps *.rpm" with python2.3 installed (comes with SuSE, but as the APBS-stuff searches for python2 in /usr/lib, it gives an error, which can be ignored of course) and it *works out of the box*. Really, really great stuff (no more GRASP/DELPHI!!!)! Bottomline: (you could add a hint on the rpm to your site stating, that they work with SuSE 9.0/9.1 (32 bit) also). Thanks for that great tool! And thanks to Warren for giving Pymol free to the world. - -- Bye, Marc Saric http://www.marcsaric.de -BEGIN PGP SIGNATURE- Version: GnuPG v1.2.4 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFA9mnxvKxJUF29wRIRAsbnAKCg3zVbI1Z8lgSgX5UbOosXYpfh/gCfRSY6 aS4Tnl9XI4FEzdMgZtba8ps= =l3cr -END PGP SIGNATURE-
Re: [PyMOL] Re: PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations
This strategy seems to work for Mandrake 9.1 too, BTW. Daniel On Thu, 2004-07-15 at 11:26, Marc Saric wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > | 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. > > Short feedback: > > I tried APBS before (when there was no plugin) but somehow ran out of > steam converting input for APBS and converting output to Pymol. > > Now I tried the Redhat-enabled rpms on SuSE 9.1 (you need to install > maloc.rpms from the maloc-site and do a "rpm -Uhv --nodeps *.rpm" with > python2.3 installed (comes with SuSE, but as the APBS-stuff searches for > python2 in /usr/lib, it gives an error, which can be ignored of course) > and it *works out of the box*. > > Really, really great stuff (no more GRASP/DELPHI!!!)! > > Bottomline: (you could add a hint on the rpm to your site stating, that > they work with SuSE 9.0/9.1 (32 bit) also). > > Thanks for that great tool! And thanks to Warren for giving Pymol free > to the world. > > > - -- > Bye, > Marc Saric http://www.marcsaric.de > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.2.4 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFA9mnxvKxJUF29wRIRAsbnAKCg3zVbI1Z8lgSgX5UbOosXYpfh/gCfRSY6 > aS4Tnl9XI4FEzdMgZtba8ps= > =l3cr > -END PGP SIGNATURE- > > > --- > 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 -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4414 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.
