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
