Hi, > I'm am a very new PYMOL user. I'm trying to calculate and display and > electrostatic map, similar to what I used to get in GRASP.
I haven't used GRASP, but I wrote the PyMOL APBS plugin, soI'll see if I can help :). > I displayed my molecule. From the 'Plugin' drop down I selected 'APBS > tools'. In 'APBS Location' tab I entered the path for apbs_tools.py for > the APBS binary location (is that correct?). Nope. APBS is a separate program for calculating electrostatics potentials. You can find it at http://agave.wustl.edu/apbs/ and you'll need to install it on your machine. > I left the APBS psize.py location blank. > > After 'set grid' and 'run APBS', I was told I needed to load a map, so I > loaded my CNS 2FomFc map. No need to load an external map here .. once you have APBS installed, you'll be able to generate everything from within PyMOL. Also, I think a 2FomFc map is an electron density map .. the Visualization tab can help you visualize any kind of map, but maybe it should say "please load an electrostatic potential map" just to make things more clear. > 'Run APBS' ran just fine, I went to the 'Visualization' tab. Actually, "Run APBS" didn't do what it was supposed to .. since you don't have APBS installed, it actually didn't do anything. I should change the APBS Plugin so that it warns you if it can't actually run APBS. In any case, you need to download and install APBS. Then, you can set it up and run it from within the APBS Plugin. Also, if your protein has any non-standard residues, you'll probably want to check the PQR file that PyMOL generates to make sure that all of the charges look reasonable. good luck, -michael > > At this point I'm confused. I've hit various 'update' buttons, the > 'Molecular Surface' on show is completely white. I've toggled values on > the visualization tab, and nothing seems to happen (even after hitting > the 'update' buttons). > > I'm hoping there is something basic I'm missing and would appreciate any > pointers. > > Many thanks, > Marilyn > > Marilyn D. Yoder > Division of Cell Biology and Biophysics > 5007 Rockhill Rd. > University of Missouri-Kansas City > Kansas City, MO 64110-2499 > phone: 816-235-1986 > fax: 816-235-1503 > > -- 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
