From: Michael B. <mb...@uv...> - 2004-09-07 17:11:27
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Okay, I think I'm getting real close to having this working (Mac G4 AlBook, OSX 10.3.5, Apple X11, X11PyMOL 0.97) Here's my simple-minded approach so far, to get electrostatics in PyMOL instead of the Honig Lab's online GRASS setup (which is also good). 1) maloc and apbs have been successfully compiled from source and installed in /usr/local 2) M. Lerner's APBS Tools plugin 'About' tab says to load a structure; the 'Visualization' tab says to load a "molecule and a map" So, I just loaded a pdb file like I usually do, and displayed as cartoon 3) set the correct location of the apbs binary (/usr/local/bin/apbs), clicked 'Set grid', then clicked 'run APBS' 4) those pink anchor handles in pymol started flashing around my protein cartoon, then a pause, then the cartoon disappeared and the pink anchors flashed around some more, then all went black. Nothing happens when I click 'Update' under the Visualization tab. 5) PyMOL output: ________________________________________________________________________ _ coarsedim is [155.64339675903321, 159.7681230545044, 272.30599403381348] finedim is [111.55493927001953, 113.98124885559082, 180.17999649047852] center is [128.19829940795898, 61.232932090759277, 21.427999496459961] finegridpoints is [225, 257, 385] radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated Hydrogens and termini so i am returning pymol-generated.pqr WARNING: 48 atoms did not have formal charges assigned WARNING: 96 atoms did not have properties assigned ObjectMapLoadDXFile-Error: Unable to open file! ________________________________________________________________________ _ supposing the WARNINGs are harmless, I'm not sure what to try next. Maybe I need the electron density map after all? --Michael |
From: Michael G. L. <ml...@um...> - 2004-09-07 19:07:36
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> 1) maloc and apbs have been successfully compiled from source and > installed in /usr/local > > 2) M. Lerner's APBS Tools plugin 'About' tab says to load a structure; > the 'Visualization' tab says to load a "molecule and a map" So, I just > loaded a pdb file like I usually do, and displayed as cartoon Fine so far. The Visualization tab is for visualizing an electrostatic potential, so it won't make sense until after you've loaded a molecule (your pdb file) and a map (most likely the electrostatic potential map that APBS generates). > 3) set the correct location of the apbs binary (/usr/local/bin/apbs), > clicked 'Set grid', then clicked 'run APBS' > > 4) those pink anchor handles in pymol started flashing around my > protein cartoon, then a pause, then the cartoon disappeared and the > pink anchors flashed around some more, then all went black. Nothing > happens when I click 'Update' under the Visualization tab. The pink dots flash around while PyMOL is assigning charges and Hydrogens. The WARNINGs later on aren't quite as harmless as you think .. they're PyMOL saying that it can't figure out how to assign charges for a number of your atoms. As far as I know, PyMOL can only assign charges for standard protein residues .. do you have any ligands or non-standard residues? Also, it looks like APBS never ran (or, if it did, it looks like APBS failed to do anything useful). What happens if you open up a command prompt in whatever directory you're working in and type /usr/local/bin/apbs pymol-generated.in ? -michael > > 5) PyMOL output: > ________________________________________________________________________ > _ > coarsedim is [155.64339675903321, 159.7681230545044, 272.30599403381348] > finedim is [111.55493927001953, 113.98124885559082, 180.17999649047852] > center is [128.19829940795898, 61.232932090759277, 21.427999496459961] > finegridpoints is [225, 257, 385] > radiobutton said to generate it Use PyMOL generated PQR and PyMOL > generated Hydrogens and termini so i am returning pymol-generated.pqr > radiobutton said to generate it Use PyMOL generated PQR and PyMOL > generated Hydrogens and termini so i am returning pymol-generated.pqr > WARNING: 48 atoms did not have formal charges assigned > WARNING: 96 atoms did not have properties assigned > ObjectMapLoadDXFile-Error: Unable to open file! > ________________________________________________________________________ > _ > > supposing the WARNINGs are harmless, I'm not sure what to try next. > Maybe I need the electron density map after all? > > --Michael > > > > ------------------------------------------------------- > 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=5047&alloc_id=10808&op=click > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > |
From: Michael B. <mb...@uv...> - 2004-09-07 19:40:43
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On Sep 7, 2004, at 3:07 PM, Michael George Lerner wrote: > Fine so far. The Visualization tab is for visualizing an electrostatic > potential, so it won't make sense until after you've loaded a molecule > (your pdb file) and a map (most likely the electrostatic potential map > that APBS generates). Oh, okay, that makes sense. And I forgot to mention before that I currently have a total of 1GB of physical RAM, but I havent tinkered with the size of swap at all, so it should be at factory default. > The pink dots flash around while PyMOL is assigning charges and > Hydrogens. > The WARNINGs later on aren't quite as harmless as you think ... do you > have any ligands or non-standard > residues? Ah yes, there are substrates bound; maybe I should remove them first from the pdb file? > Also, it looks like APBS never ran (or, if it did, it looks like APBS > failed to do anything useful). What happens if you open up a command > prompt in whatever directory you're working in and type > "/usr/local/bin/apbs pymol-generated.in" ? I get the following info, with a couple errors at the end: ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 0.3.1 Nathan A. Baker (ba...@bi...) Dept. Biochemistry and Molecular Biophysics Center for Computational Biology Washington University in St. Louis Additional contributing authors listed in the code documentation. Copyright (c) 2002-2004. Washington University in St. Louis. All Rights Reserved. Portions Copyright (c) 1999-2002. The Regents of the University of California. Portions Copyright (c) 1995. Michael Holst. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ---------------------------------------------------------------------- This executable compiled on Sep 2 2004 at 16:32:37 Vio_ctor2: some error occurred. Vio_ctor: Vio_ctor2() failed. Parsing input file pymol-generated.in... NOsh_parse: Got pointer to NULL socket! Error while parsing input file. |