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] sequence visualisation bug ?
Hi all When I visualise sequences, all Glu residues (as well as all Asp residues) are shown as D! Has anyone else seen this? Daniel -- 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] sequence visualisation bug ?
Yes, I've got the same problem. Jules Daniel Rigden wrote: Hi all When I visualise sequences, all Glu residues (as well as all Asp residues) are shown as D! Has anyone else seen this? Daniel
[PyMOL] selection of residues with negative numbers
Hi All- I cannot make PyMOL make selections of residues with negative (sequence) numbers. Any quick way around this? ex. that works: PyMOLshow sticks, //mod1//10/ ex. that fails: PyMOLshow sticks, //mod1//-4/ Selector-Error: Invalid Range. ( s; mod1 i; :4 )-- I found this post on the mailing list, but no responses were posted: http://sourceforge.net/mailarchive/message.php?msg_id=4223049 Thanks! Doug
RE: [PyMOL] selection of residues with negative numbers
Douglas, I don't think PyMOL can handle negative selections yet. Just make them positive: alter all, resi=int(resi)+100 etc. 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 Douglas Kojetin Sent: Thursday, July 15, 2004 8:23 AM To: pymol Subject: [PyMOL] selection of residues with negative numbers Hi All- I cannot make PyMOL make selections of residues with negative (sequence) numbers. Any quick way around this? ex. that works: PyMOLshow sticks, //mod1//10/ ex. that fails: PyMOLshow sticks, //mod1//-4/ Selector-Error: Invalid Range. ( s; mod1 i; :4 )-- I found this post on the mailing list, but no responses were posted: http://sourceforge.net/mailarchive/message.php?msg_id=4223049 Thanks! Doug --- 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=4721alloc_id=10040op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] Problem in sequence viewer for GLU
Hi, I found a little bug in the sequence viewer in the Pymol version 0.96 for linux: All glutamic acid (E) are identified by the aspartic acid letter (D). But the sequence is readed correctly, because when I color my GLU (color yellow, resn GLU) the D become yellow in the sequence viewer. Cheers, Olivier -- Olivier Julien Étudiant en biochimie Laboratoire Dr Stéphane Gagné (CREFSIP) 3252 Pav. Marchand Université Laval Tel: (418) 656-2131 #4530 Fax: (418) 656-7176 e-mail: ojul...@rsvs.ulaval.ca
[PyMOL] A couple of quick PyMOL + APBS notes
Hi all, I've been getting two questions about APBS from a few people, so I thought I'd send the answers here: 1) Does APBS take a lot of memory? APBS can certainly take a lot of memory. In addition, my plugin sets up a grid that's a little finer than the APBS default (more grid points == better calculation, but more memory). You can point my plugin at APBS's version of psize.py for a grid setup that'll use less memory, and I'll add some more options in the next version of the plugin that'll make it easier to set up a coarser grid. 2) Does it work on a Mac? My plugin should work with Macs just fine. And Nathan Baker just posted this to the APBS list: Hi All -- Thanks to Michael Grabe (UCSF), temporary Mac G4 and G5 binaries are available from the APBS download website while we try to get our G5 up and running. So it sounds like it should be much easier to set things up now! Thanks, -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
Re: [PyMOL] A couple of quick PyMOL + APBS notes
The reason it doesn't work is because, I think, APBS was not compiled by the fink g77. More likely it was compiled by a g77 from http://hpc.sourceforge.net/ or other similar places. So you need to install that version of g77 to get APBS running on you mac. If anybody can compiled APBS using fink g77, that will be great. Jianghai == Jianghai Zhu Molecular Biology Biochemistry Purdue University == On Jul 15, 2004, at 6:52 PM, Douglas Kojetin wrote: (this might be better suited on an APBS list, but i figured i'd give it a shot here) I downloaded the Mac APBS binary, but I'm seeing this error when trying to run it: % ./apbs-0.3.1-g4 dyld: ./apbs-0.3.1-g4 can't open library: /usr/local/lib/libg2c.0.dylib (No such file or directory, errno = 2) Trace/BPT trap Anyone else see this or know how to overcome it? Thanks, Doug On Jul 15, 2004, at 7:33 PM, Michael George Lerner wrote:
Re: [PyMOL] A couple of quick PyMOL + APBS notes
Verified. I downloaded the g77 available from http://hpc.sourceforge.net, copied the files to the respective directories in /usr/local/, and the binary appears to work now (at least no errors when I run it with no input as before). Thanks! Doug On Jul 15, 2004, at 8:02 PM, Jianghai Zhu wrote: The reason it doesn't work is because, I think, APBS was not compiled by the fink g77. More likely it was compiled by a g77 from http://hpc.sourceforge.net/ or other similar places. So you need to install that version of g77 to get APBS running on you mac. If anybody can compiled APBS using fink g77, that will be great. Jianghai == Jianghai Zhu Molecular Biology Biochemistry Purdue University == On Jul 15, 2004, at 6:52 PM, Douglas Kojetin wrote: (this might be better suited on an APBS list, but i figured i'd give it a shot here) I downloaded the Mac APBS binary, but I'm seeing this error when trying to run it: % ./apbs-0.3.1-g4 dyld: ./apbs-0.3.1-g4 can't open library: /usr/local/lib/libg2c.0.dylib (No such file or directory, errno = 2) Trace/BPT trap Anyone else see this or know how to overcome it? Thanks, Doug On Jul 15, 2004, at 7:33 PM, Michael George Lerner wrote: --- 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=4721alloc_id=10040op=click ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
