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.
