Re: [PyMOL] Visualizing two surfaces using APB2tools2.1
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
Re: [PyMOL] Visualizing two surfaces using APB2tools2.1
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
Re: [PyMOL] Visualizing two surfaces using APB2tools2.1
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) -- 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
[PyMOL] Visualizing two surfaces using APB2tools2.1
Hello, Does anyone know how to visualize the surface potentials of two molecules simoutaneously using the APBS Tools2.1 plugin? Thanks. -Yarrow -- 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
