Thank you very much. I had trouble with Jason's method but the second one worked great! Now I have beautifull e-static surfaces to show at my talk. Thank you!
-Yarrow > Thanks for the nice writeup, Jason! > > There are two main ways that I know of to visualize two potentials at > once. > This is one. If you're looking at, e.g., a protein-protein interface, it > may > be useful to map two different electrostatic potentials to two different > PyMOL objects. Here's my overly-cautious recipe for doing that: > > 1. Load up PyMOL with one of your structures. > 2. Fire up the plugin. Click on "Choose Externally Generated PQR File" and > point it at your PQR file. > 3. Click on the Temp File Locations tab and change the name of the > temporary > DX file to something meaningful, e.g. structure1.dx > 4. Set grid and Run APBS as normal. > 5. Close the plugin. > 6. Type "delete all" > 7. Load up the second structure. > 8. Repeat steps 2-4, changing the name to something like structure2.dx > this > time. > > Now you have two correctly generated electrostatics potential maps (note: > the reason I had you do things with one structure at a time loaded in > PyMOL > is so that you wouldn't have to fiddle around with the "Selection to use" > section of the Main options tab). Use the load command to load up the > other > pqr file and the other dx map, then use the visualization panes as normal. > > Cheers, > > -Michael > > On Tue, Feb 1, 2011 at 9:48 AM, Jason Vertrees < > jason.vertr...@schrodinger.com> wrote: > >> Hi Yarrow, >> >> > Does anyone know how to visualize the surface potentials of two >> molecules >> > simoutaneously using the APBS Tools2.1 plugin? Thanks. >> >> As Michael wrote the APBS plugin, he might have more to offer, but >> here's how I'd do it. I used this technique to look at two similar >> proteins side-by-side in PyMOL (see the 2nd image on >> http://www.pymolwiki.org/index.php/APBS). The trick is to (1) use >> grid_mode and grid_slots; and (2) rename the maps as appropriate. >> It's not hard, but will take a couple minutes. Here's how: >> >> # get two proteins; use whatever you like >> fetch 1rx1 1rx2, async=0 >> >> # put them in the same frame of reference for grid mode >> align 1rx1, 1rx2 >> >> # run APBS on protein #1, 1rx1 >> Plugin > APBS Tools2 > ... >> Under "selection to use" type "(polymer) and 1rx1" >> >> # rename the map >> set_name pymol-generated, 1rx1_map >> >> # run APBS on protein 2, 1rx2; remove the waters >> Plugin > APBS Tools2 >> Under "selection to use" type "(polymer) and 1rx2" >> >> # rename the map >> set_name pymol-generated, 1rx2_map >> >> # Now, using APBS show the surfaces make sure you choose >> # 1rx1_map for 1rx1 and 1rx2_map for 1rx2; click "Update" if those >> # map names are not present. >> ... >> >> # turn on grid mode >> set grid_mode >> >> # assign grid slots just to be sure the right maps >> # and proteins are in the right places >> set grid_slot, 1, 1rx1 >> set grid_slot, 1, 1rx1_map >> set grid_slot, 1, e_lvl_0_1 >> >> set grid_slot, 2, 1rx2 >> set grid_slot, 2, 1rx2_map >> set grid_slot, 2, e_lvl_1_1 >> >> >> Now, you should be set and have an image like that I posted on the >> PyMOLWiki. >> >> Cheers, >> >> -- Jason >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) jason.vertr...@schrodinger.com >> (o) +1 (603) 374-7120 >> >> >> ------------------------------------------------------------------------------ >> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! >> Finally, a world-class log management solution at an even better >> price-free! >> Download using promo code Free_Logger_4_Dev2Dev. Offer expires >> February 28th, so secure your free ArcSight Logger TODAY! >> http://p.sf.net/sfu/arcsight-sfd2d >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > > -- > Michael Lerner, Ph.D. > IRTA Postdoctoral Fellow > Laboratory of Computational Biology NIH/NHLBI > 5635 Fishers Lane, Room T909, MSC 9314 > Rockville, MD 20852 (UPS/FedEx/Reality) > Bethesda MD 20892-9314 (USPS) > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 ------------------------------------------------------------------------------ Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
