> 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 > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
