From: Marc S. <mar...@gm...> - 2004-07-15 11:26:51
|
-----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----- |
From: Michael G. L. <ml...@um...> - 2004-07-15 23:33:21
|
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 | / \ | mlerner@umich |
From: Douglas K. <djk...@un...> - 2004-07-15 23:52:57
|
(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: > > 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! |
From: Jianghai Z. <zh...@pu...> - 2004-07-16 00:02:48
|
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: > |
From: Douglas K. <djk...@un...> - 2004-07-16 00:19:57
|
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=4721&alloc_id=10040&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: James S. <jst...@sc...> - 2004-07-16 00:19:19
|
I get this too....all very depressing......enough to put one off Unix for good......just joking. J ---------------------------------------- Dr. James Stevens Senior Research Associate Department of Molecular Biology - BCC206 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA ---------------------------------------- Tel. (858)-784-9878 Fax. (858)-784-2980 E-mail. jst...@sc... ---------------------------------------- On Thu, 15 Jul 2004, 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: > > > > > 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! > > > > ------------------------------------------------------- > 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 > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Daniel R. <dr...@li...> - 2004-07-16 10:34:22
|
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 > PyM...@li... > 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. |