Re: [PyMOL] Dot representation
Thanks Jared. On Mon, Jan 5, 2015 at 1:35 PM, Sampson, Jared jared.samp...@nyumc.org wrote: Hi Yarrow - 1. Yes, according to the wiki http://www.pymolwiki.org/index.php/Dots, the dots are located on the vdW surface unless the `dot_solvent` setting is turned on (in which case they’re on the solvent accessible surface). 2. Based on the settings listed with “dot” in their names, it doesn’t look like dot_transparency is currently available. Hope that helps. Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center http://kong.med.nyu.edu/ On Dec 30, 2014, at 6:48 PM, Yarrow Madrona acacia.madr...@ucsf.edu wrote: Hell Pymolers, 1. Does anyone know what the dot representation for a residue represents? Is it the van der waals radii? 2. Is there a way to draw transparency for the dots? -Yarrow -- Yarrow Madrona, Ph.D. *Postdoctoral Scholar* University of California, San Francisco Department of Pharmaceutical Chemistry Rm N551, 600 16th street San Francisco CA, 94143 -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ 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 -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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 -- Yarrow Madrona, Ph.D. *Postdoctoral Scholar* University of California, San Francisco Department of Pharmaceutical Chemistry Rm N551, 600 16th street San Francisco CA, 94143 -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ 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] Scripting attempts
Sorry, I didn't read the other entries. Thanks for the python end code. I have had this problem with loops a lot in pymol and this solves it. -Yarrow On Tue, Jan 6, 2015 at 9:21 AM, Yarrow Madrona acacia.madr...@ucsf.edu wrote: Hi Brenton, I'm pretty sure you have to import python in your script. Otherwise the python commands will be ignored. Also you forgot to put colons after your 'for' statement. Either way, I think pymol got the first image then ignored the 'for statement' and just went straight to the second 'png.' which it named %4d because you didn't tell it to recognize python string formatting by importing python. -Yarrow On Tue, Jan 6, 2015 at 6:00 AM, Brenton Horne brentonho...@ymail.com wrote: Hi, I've been executing the pml script I wrote: set ray_opaque_background, 0 png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1 for i in range(2, 60) rotate y, 6 png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL movie\Image%4d.png, dpi=300, ray=1 The desired result from this script is a series of 60 transparent pngs taken at 6 degrees apart (rotated around the y axis) with name Image0001.png, Image0002.png, Image0003.png, ..., Image0060.png. Sadly however I only got two PNGs: Image0001.png and Image%4d.png. How do I overcome this problem? Thanks for your time, Brenton -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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 -- Yarrow Madrona, Ph.D. *Postdoctoral Scholar* University of California, San Francisco Department of Pharmaceutical Chemistry Rm N551, 600 16th street San Francisco CA, 94143 -- Yarrow Madrona, Ph.D. *Postdoctoral Scholar* University of California, San Francisco Department of Pharmaceutical Chemistry Rm N551, 600 16th street San Francisco CA, 94143 -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ 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] Scripting attempts
Hi Brenton, I'm pretty sure you have to import python in your script. Otherwise the python commands will be ignored. Also you forgot to put colons after your 'for' statement. Either way, I think pymol got the first image then ignored the 'for statement' and just went straight to the second 'png.' which it named %4d because you didn't tell it to recognize python string formatting by importing python. -Yarrow On Tue, Jan 6, 2015 at 6:00 AM, Brenton Horne brentonho...@ymail.com wrote: Hi, I've been executing the pml script I wrote: set ray_opaque_background, 0 png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL movie\Image0001.png, dpi=300, ray=1 for i in range(2, 60) rotate y, 6 png C:\Users\Brenton\Documents\Chem Structures\PDBs\2\2HYY - imatinib\PyMOL movie\Image%4d.png, dpi=300, ray=1 The desired result from this script is a series of 60 transparent pngs taken at 6 degrees apart (rotated around the y axis) with name Image0001.png, Image0002.png, Image0003.png, ..., Image0060.png. Sadly however I only got two PNGs: Image0001.png and Image%4d.png. How do I overcome this problem? Thanks for your time, Brenton -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net ___ 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 -- Yarrow Madrona, Ph.D. *Postdoctoral Scholar* University of California, San Francisco Department of Pharmaceutical Chemistry Rm N551, 600 16th street San Francisco CA, 94143 -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ 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] Dot representation
Hell Pymolers, 1. Does anyone know what the dot representation for a residue represents? Is it the van der waals radii? 2. Is there a way to draw transparency for the dots? -Yarrow -- Yarrow Madrona, Ph.D. *Postdoctoral Scholar* University of California, San Francisco Department of Pharmaceutical Chemistry Rm N551, 600 16th street San Francisco CA, 94143 -- Dive into the World of Parallel Programming! The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net___ 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] surface transparency not chaning
Hello Pymol users, As anyone experienced an instance where the surface transparency remained stuck in one color? I changed it to pink a while back. However, now issuing the comand: set surface_color, green, object1 does nothing. Object1 is the object I want to color. Even if I try to change the surface color globally it doesn't work (set surface_color, green, all) I would appreciate any help I can receive. Thank you. -Yarrow -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds___ 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] surface stuck on one color
I think the problem may have to do with the surface_cavity_mode being set to 3. I try to change the surface_cavity_mode but I still detect cavities instead of the surface. It seems like any option related to the surface is locked. -Yarrow -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds___ 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] surface stuck on one color
Hi Pymolers I have solved my problem. I am using surface cavity_mode, 3. I need to change the ray_interior_color instead of the surface color. I guess this is because pymol is visualizing the interior of the surface not the exterior. -Yarrow On Thu, Jul 24, 2014 at 11:08 AM, Yarrow Madrona amadr...@uci.edu wrote: I think the problem may have to do with the surface_cavity_mode being set to 3. I try to change the surface_cavity_mode but I still detect cavities instead of the surface. It seems like any option related to the surface is locked. -Yarrow -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds___ 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] Portein cross section
Hello, I have previously cut my protein in half with a solid cross section using a series of steps (including photoshop) but I am wondering if there is something simpler. I would like to make a figure similar to this: https://www.dropbox.com/s/bxpz6v4xly5fsee/MMI_7243_f6.gif This can be done pretty easily in Chimera, but I already have everything in Pymol and would like not to have to repeat it all. Thank you. -- Time is money. Stop wasting it! Get your web API in 5 minutes. www.restlet.com/download http://p.sf.net/sfu/restlet___ 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] script with arguments.
Hello, I am making a script that loads in two molecules as arguments in the command line. I want to then align these molecules and make a pretty picture of the molecules that were input as arguments in the comand line but I am not sure how to name them as objects. I don't know how to select the new objects because they will have different names depending on the inputed arguments. My attempt is below. -Yarrow -- from sys import argv my_argv = argv[1:] print my_argv[0], my_argv[1] from pymol import cmd, stored def align_heme(arg1, arg2 ): cmd.load(arg1) cmd.load(arg2) cmd.create(obj1, arg1) #I know this line won't work. I need to use the#object name. but it depends on the input. -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231iu=/4140/ostg.clktrk___ 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] trouble with sym exp
Hello pymol users, I am trying to generate symetry related molecules for a molecule in space group P322 with one molecule in the ASU. unfortunately I get a lot of clashes with the symmetry mates and wrong contacts that just are not there when visualizing in coot. I wonder if this is a problem of pymol? Can I feed it the symmetry operators instead? -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ 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] internal cavity lighting
Thanks Thomas! This is exactly what I was looking for. -Yarrow Hi Yarrow and Patrice, PyMOL introduced ambient occlusion in version 1.5.0 for surface rendering. Try this: fetch 1rx1, async=0 as surface set ambient_occlusion_mode If you are a pymol sponsor, visit this page: http://pymol.org/dsc/dokuwiki/doku.php?id=media:ambient_occlusion Hope that helps. Cheers, Thomas Patrice Peterson wrote, On 05/29/13 13:37: On 13-05-28 14:11, Yarrow Madrona wrote: Hi, I saw a post on this sight a while back about how to move the lighting. However, I have not seen any information on how to change the lighting of an internal cavity. I want the internal cavity to appear darker as it would be more realistic. However, it is almost like there is a light source coming from inside the object that brightens it up. Does anyone know how to change the internal lighting of a cavity when shown in surface representation? Thanks. Hey, What you probably want is some kind of ambient occlusion. The tachyon rendering library (which is used with VMD) can do that. However, you can get a similar effect in PyMOL using the POV-Ray renderer with appropriate radiosity settings. I'm using a modified make_pov.py script to do something similar [1], but the POV-Ray settings are not yet finalized (I'm very new to POV-Ray myself). I'd also suggest using POV-Ray 3.7 to allow the use of multiple cores, as radiosity can increase rendering time quite significantly. The file I posted does not yet have the correct field of view. I'll update the Gist once I've found the correct value. Cheers, Patrice [1] https://gist.github.com/runiq/5669624 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ 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 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ 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] internal cavity lighting
Thanks Patrice, I have used VMD mostly to look at trajectories. I should delve into in a bit more. I really like having a one stop-shop for illustration which is why I like pymol. However, I have heard a lot about POV-ray and want to explore it. I have also heard that it is a black-hole and very difficult. Still maybe worth it. -Yarrow On 13-05-28 14:11, Yarrow Madrona wrote: Hi, I saw a post on this sight a while back about how to move the lighting. However, I have not seen any information on how to change the lighting of an internal cavity. I want the internal cavity to appear darker as it would be more realistic. However, it is almost like there is a light source coming from inside the object that brightens it up. Does anyone know how to change the internal lighting of a cavity when shown in surface representation? Thanks. Hey, What you probably want is some kind of ambient occlusion. The tachyon rendering library (which is used with VMD) can do that. However, you can get a similar effect in PyMOL using the POV-Ray renderer with appropriate radiosity settings. I'm using a modified make_pov.py script to do something similar [1], but the POV-Ray settings are not yet finalized (I'm very new to POV-Ray myself). I'd also suggest using POV-Ray 3.7 to allow the use of multiple cores, as radiosity can increase rendering time quite significantly. The file I posted does not yet have the correct field of view. I'll update the Gist once I've found the correct value. Cheers, Patrice [1] https://gist.github.com/runiq/5669624 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1___ 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 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ 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] Can CAVER be run iteratively through a python script?
Hi Sajeewa, I just did the same thing using CAVER3.0. You can download it from their website. You save the snapshots as sequential PDB's and CAVER takes care of the rest. You can get very good documentation and step by step guides from their website. -Yarrow Hi all, I have a few hundred pdb snapshots of a protein in which I have to check a tunnel with the same starting point. Without opening them one by one and running CAVER separately for each snapshot, is there any way to run CAVER iteratively using a Python script? If there is, it would save me loads of time. Thank you Sajeewa Dewage -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ 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 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ 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] [Pymol] plugins won't intitialize
Hello, Does anyone know why plugins wont initialize. I get the following message when trying to install movs.py into pymol1.5: Exception in plugin 'movs' -- Traceback follows... Traceback (most recent call last): File /Applications/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/PMGApp.py, line 320, in initializePlugins mod.__init__(self) TypeError: module.__init__() argument 1 must be string, not instance Error: unable to initialize plugin 'movs'. I guess there is something wrong with the code but this seems strange. It looks o.k. Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ 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] How to ray trace clipped image without clipping spheres.
Hi, Does anyone know how to ray trace an image of an active site in sphere representation that is clipped, without getting a weird result that I assume comes from clipping the spheres? It looks like unfilled circles. Thank you -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester Wave(TM): Endpoint Security, Q1 2013 and remains a good choice in the endpoint security space. For insight on selecting the right partner to tackle endpoint security challenges, access the full report. http://p.sf.net/sfu/symantec-dev2dev ___ 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] [PyMol] How to visualize surface within a given radius
Thank you both for your kind help. I will follow this up today and let you know how it goes. -Yarrow Greetings, Please also investigate the following settings: # needs a real atom selection surface_carve_selection # distance from the above selection to cull surfaces surface_carve_cutoff I looked at your data and there is a small problem. You have a few points where one atom is mapped to multiple surface points. Thus, when you show it as surface two pocket fragments show up. When you hide it they both hide. Also of interest is PyMOL's ability to render pockets and cavities on its own (Settings Surface Cavities Pockets). Cheers, -- Jason On Mon, Mar 4, 2013 at 2:15 PM, Sampson, Jared jared.samp...@nyumc.orgwrote: Hi Yarrow - If you add br. to the show surface command, you will get more continuous surfaces, as the selection will be made by residue instead of by atom. show surface, br. protein within 0.5 of pocket_selection If you don't want to show the surface from a particular residue (e.g. if it's masking something else you want to show), you can hide surface for a selection. hide surface, resi 225+347 Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Mar 4, 2013, at 2:37 PM, Yarrow Madrona amadr...@uci.edu wrote: Thank you for your help Thomas, Using your settings I get a lot of partial surfaces Showing the surface around the Pocket selection like this: show surface, protein within 0.5 of pocket_selection worked well but I still see a piece of surface that I really don't want to show up. I guess I can take it out in photoshop but that just seems wrong. I have attached it. -Yarrow Hi Yarrow, should be as simple as: PyMOL hide surface PyMOL show surface, (organic around 8.0) PyMOL set transparency, 0.3 PyMOL set two_sided_lighting See also: http://pymolwiki.org/index.php/Selection_Algebra Hope that helps. Cheers, Thomas Yarrow Madrona wrote, On 03/03/13 18:34: Hello, Does anyone know how to visualize a surface within a given radius from a ligand binding site? In chimera you can limit the display surface within 0-X angstrom of a ligand. This allows you to see the surface surrounding the ligand without the rest of the protein. I guess you could create a new selection of residues around a ligand and show this surface but I wondered if there are any other ways of doing this. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 screenshot.png -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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 -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page
Re: [PyMOL] [PyMol] How to visualize surface within a given radius
Thank you for your help Thomas, Using your settings I get a lot of partial surfaces Showing the surface around the Pocket selection like this: show surface, protein within 0.5 of pocket_selection worked well but I still see a piece of surface that I really don't want to show up. I guess I can take it out in photoshop but that just seems wrong. I have attached it. -Yarrow Hi Yarrow, should be as simple as: PyMOL hide surface PyMOL show surface, (organic around 8.0) PyMOL set transparency, 0.3 PyMOL set two_sided_lighting See also: http://pymolwiki.org/index.php/Selection_Algebra Hope that helps. Cheers, Thomas Yarrow Madrona wrote, On 03/03/13 18:34: Hello, Does anyone know how to visualize a surface within a given radius from a ligand binding site? In chimera you can limit the display surface within 0-X angstrom of a ligand. This allows you to see the surface surrounding the ligand without the rest of the protein. I guess you could create a new selection of residues around a ligand and show this surface but I wondered if there are any other ways of doing this. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 attachment: screenshot.png-- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ 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] [PyMol] How to visualize surface within a given radius
Hello, Does anyone know how to visualize a surface within a given radius from a ligand binding site? In chimera you can limit the display surface within 0-X angstrom of a ligand. This allows you to see the surface surrounding the ligand without the rest of the protein. I guess you could create a new selection of residues around a ligand and show this surface but I wondered if there are any other ways of doing this. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] How to visualize an active site pocket using specific residues?
Hello, I have some output from the CASTp server-pymol plugin. I have the residues selected surrounding an active site pocket. I would like to make a shape with these atoms as vertices that I can color transparent from the atom selection. Is there a way to do this in pymol? Thank you. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] ccp4 map sigma setting
Hi, When I display ccp4 maps in pymol they look a bit larger than I am used to seeing in coot for a given sigma setting. Is it common for users to increase the sigma setting when displaying maps in pymol? -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ 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] changing ray_trace_line
Hello, This seems to be a simple problem but I can't figure out how to change the outline width of the ray_trace in ray_trace_mode, 1. I want to make it thicker so that when I ray_trace it doesn't look so small. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] changing ray_trace_line
Hi Thomas, I have tried this. It works well for sticks but puts a lot of cross hatching patterns in the cartoon representation. I would like to ray_trace a transparent or white cartoon without the hatching (looks like shading drawn with ink) -Yarrow Hi Yarrow, you are looking for the ray_trace_gain setting. http://pymolwiki.org/index.php/Ray_Trace_Gain Cheers, Thomas Yarrow Madrona wrote, On 05/17/12 21:11: Hello, This seems to be a simple problem but I can't figure out how to change the outline width of the ray_trace in ray_trace_mode, 1. I want to make it thicker so that when I ray_trace it doesn't look so small. -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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
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
[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
