Re: [PyMOL] Select crystal waters inside protein
Dear PyMOL Users I'm trying to remove water molecules from a crystal structure which are on the crystal surface while preserving the ones within the crystal interior. What I do is: select waters, resn HOH # cmd.select(waters, (waters extend 1), enable=1) get_area waters, load_b=1 remove waters and b20 This only works partially because of some waters, only the oxygen atom is removed, while of others only one of the hydrogens is removed (some waters are completely removed which is good). It does not make a difference if I include the commented command above. Also, what does load_b=1 mean? Further feedback would be greatly appreciated. Martin On 26.04.12 14:46, Thomas Holder wrote: Hi Martin James, is it just a coincident that you both ask almost the same question? You could remove all water atoms with few protein contacts or with a small surface area. For example: remove solvent beyond 3.5 of polymer set dot_solvent get_area solvent, load_b=1 remove solvent and b 20 Hope that helps. Cheers, Thomas On 04/26/2012 10:55 AM, James Starlight wrote: Another question- I have my protein.pdb with some inserted crystall waters within protein interiour as well as water surrounded of my protein. I want to remove only sorrounding water but prevent internal water ( wich could be functional relevant ). How I could to select such surrounded water ( e.g via some cutoff radius relative my protein etc) wich I'd like to remove further ? On 04/25/2012 05:34 PM, Martin Hediger wrote: In a crystal structure, there are usually a number of relevant crystal waters, as well as water molecules on the surface. In our approach, we model the protein structure within a dielectric continuum, so surface water molecules are not required (to save computer time). However, waters in the interior should remain in our model. How could we discard the surface waters while keeping the internal waters? -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-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] Select crystal waters inside protein
Hi Martin, 2012/10/4 Martin Hediger ma@bluewin.ch Dear PyMOL Users I'm trying to remove water molecules from a crystal structure which are on the crystal surface while preserving the ones within the crystal interior. What I do is: select waters, resn HOH # cmd.select(waters, (waters extend 1), enable=1) get_area waters, load_b=1 remove waters and b20 This only works partially because of some waters, only the oxygen atom is removed, while of others only one of the hydrogens is removed (some waters are completely removed which is good). It does not make a difference if I include the commented command above. You might want to read up on the selection algebra of PyMOL ( http://www.pymolwiki.org/index.php/Selection_Algebra) which is quite powerfull. You can use the by residue selection to select the entire residue that fits you description, so in your case remove byres waters and b20 Will remove every residues within your selection waters, where at least one atom has a b factor of more than 20. (and of course now you have altered the b factor according to the calculated surface area) Also, what does load_b=1 mean? http://www.pymolwiki.org/index.php/Get_Area It is explained in the last example (3) load_b=1 will put the value of the surface area into the b factor column. Hope that helps! Best regards, Folmer Further feedback would be greatly appreciated. Martin On 26.04.12 14:46, Thomas Holder wrote: Hi Martin James, is it just a coincident that you both ask almost the same question? You could remove all water atoms with few protein contacts or with a small surface area. For example: remove solvent beyond 3.5 of polymer set dot_solvent get_area solvent, load_b=1 remove solvent and b 20 Hope that helps. Cheers, Thomas On 04/26/2012 10:55 AM, James Starlight wrote: Another question- I have my protein.pdb with some inserted crystall waters within protein interiour as well as water surrounded of my protein. I want to remove only sorrounding water but prevent internal water ( wich could be functional relevant ). How I could to select such surrounded water ( e.g via some cutoff radius relative my protein etc) wich I'd like to remove further ? On 04/25/2012 05:34 PM, Martin Hediger wrote: In a crystal structure, there are usually a number of relevant crystal waters, as well as water molecules on the surface. In our approach, we model the protein structure within a dielectric continuum, so surface water molecules are not required (to save computer time). However, waters in the interior should remain in our model. How could we discard the surface waters while keeping the internal waters? -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-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 -- Folmer Fredslund -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-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] bond connection file
Hi Vishwas, you can use PDB format with CONECT records. You need to set connect_mode=1 before loading the PDB file into PyMOL. http://pymolwiki.org/index.php/Connect_mode http://www.wwpdb.org/documentation/format33/sect10.html#CONECT Hope that helps. Cheers, Thomas Vishwas Vasisht wrote, On 10/04/12 16:52: Hi, I want to feed in a coordinates of atoms along with bond connection information. Since the bonding is based on some calculation I do, I need to include this information by hand. I tried to output the trajectory from my analysis in .mol format (following some example .mol file), but particles are overlapping on each other. Can somebody suggest me a better way to feed in coordinates and bonding information to pymol. Regards Vishwas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-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] I just built pymol, comes up but hangs on any attempt to view a test pdb.
fwiw, I never figured out why the out-of-the-box build hung using the python approach but I went through the ./cogifure, make make install route and did get the test molecules to display. However, I ran into lots of problems with the ShaderMgr and ccealignmodule and then finally the link was missing -lGLEW. In any case it looks like I am all set but I thought the download would come closer to working right away. And the xyz files I wanted to display do appear to come up just great. So do I need a license for the open source version? Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave message 989-348-4796 (P)- emergency From: marchy...@hotmail.com To: pymol-users@lists.sourceforge.net Date: Thu, 4 Oct 2012 15:43:53 -0400 Subject: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. Is there some common reason for this? CPU on one core stays at 100 percent and no more menu's come up. The larger window says at the bottom that the version is supposed to be licensed but I just pulled it down from sourceforge and not sure that this version needs a key to work. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave message 989-348-4796 (P)- emergency -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-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] I just built pymol, comes up but hangs on any attempt to view a test pdb.
CC: pymol-users@lists.sourceforge.net From: li...@cowsandmilk.net Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. Date: Thu, 4 Oct 2012 22:03:59 -0400 To: marchy...@hotmail.com You don't need a license for the open source version. If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. Well, I thought there may be a dev list or something for the most of this stuff but in any case I'm on Ubuntu but that probably was not a big factor for some of the issues I ran into I just wanted to display 2 molecules side by side and could not get jmol or gdis to work right away and someone suggested this. ( fwiw, I have my own molecule viewer that IIRC I wrote to learn glut on cygwin but I imagine that would be an even bigger chore to port LOL). If I can reconstruct, I apparently started with pymol-v1.5.0.1.tar and I think at some point I ran autoreconf -l thinking I could go the configure route but then did python setup.py build and install in separeate steps., This seemed to work but attempts to display the test pdb files never displayed anything, I could not get any more menu's and one core was running at 100 percent until I killed it. Going the confugre route, I think the first problem was with a bunch of undefined CGO things. but you can see the changes below. The EXT thing was spurious probably as there was a missing -lGLEW and I had to relink. This is obviously a raw dump of things that I tried along with stuff that ultimately worked but fwiw. marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name *.h ./layer0/os_gl.h ./contrib/uiuc/plugins/include/molfile_plugin.h ./generated/include/ShaderText.h ./config.h marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ find -mtime -2 -name *.c ./layer0/ShaderText.c ./layer0/ShaderMgr.c ./layer3/Executive.c ./generated/src/ShaderText.c ./layer2/ObjectVolume.c ./layer1/CGO.c ./layer1/Scene.c marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find -mtime -2 -name *.c ` ./layer0/ShaderMgr.c:97: FeedbackAdd(G, mjm forcing glew ok Shaders available.\n); ./layer0/ShaderMgr.c:98:// this should work but turn off for now mjm ./layer0/ShaderMgr.c-99-// if (GLEW_VERSION_2_0) ./layer0/ShaderMgr.c-100- if (1) -- ./layer3/Executive.c:76:// mjm ./layer3/Executive.c-77-#includemodules/cealign/src/ce_types.h ./layer3/Executive.c-78-/* Externals for CEAlign */ -- ./layer1/Scene.c:2910://mjm ./layer1/Scene.c-2911- 1.0F, 1.0F, 0.1F, 1.f ./layer1/Scene.c-2912- }; -- ./layer1/Scene.c:1: //mjm ./layer1/Scene.c-10001-//glBlitFramebufferEXT (0, 0, I-offscreen_width / 2, I-offscreen_height, ./layer1/Scene.c-10002- glBlitFramebuffer (0, 0, I-offscreen_width / 2, I-offscreen_height, -- ./layer1/Scene.c:10007://mjm ./layer1/Scene.c-10008- glBlitFramebuffer (I-offscreen_width / 2, 0, I-offscreen_width, I-offscreen_height, ./layer1/Scene.c-10009- //glBlitFramebufferEXT (I-offscreen_width / 2, 0, I-offscreen_width, I-offscreen_height, -- ./layer1/Scene.c:10016: //mjm ./layer1/Scene.c-10017- //glBlitFramebufferEXT (0, 0, I-offscreen_width, I-offscreen_height, ./layer1/Scene.c-10018- glBlitFramebuffer (0, 0, I-offscreen_width, I-offscreen_height, -- ./layer1/Scene.c:10024: //mjm ./layer1/Scene.c-10025-// glBlitFramebufferEXT (0, 0, I-offscreen_width, I-offscreen_height, ./layer1/Scene.c-10026- glBlitFramebuffer (0, 0, I-offscreen_width, I-offscreen_height, marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ grep -n -A 2 mjm `find -mtime -2 -name *.h ` ./layer0/os_gl.h:6:// mjm ./layer0/os_gl.h-7-//#if defined(_PYMOL_IOS) || defined(ANDROID) ./layer0/os_gl.h-8-#if 1 ./layer0/os_gl.h:9:// mjm ./layer0/os_gl.h-10-// #define _PYMOL_PURE_OPENGL_ES ./layer0/os_gl.h-11-#define _PYMOL_CGO_DRAWARRAYS -- ./contrib/uiuc/plugins/include/molfile_plugin.h:249:// mjm - these are in the games lass LOL ./contrib/uiuc/plugins/include/molfile_plugin.h-250-int have_esp; ./contrib/uiuc/plugins/include/molfile_plugin.h-251-int have_npa; -- ./contrib/uiuc/plugins/include/molfile_plugin.h:312:// mjm ./contrib/uiuc/plugins/include/molfile_plugin.h-313-int multiplicity; ./contrib/uiuc/plugins/include/molfile_plugin.h-314-int * esp_charges; marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ marchywka@marchywka-Latitude-E6510:~/d/pymol/pymol$ cat relink gcc --verbose -shared -fPIC -DPIC -Wl,--no-as-needed -Wl,--whole-archive contrib/uiuc/plugins/molfile_plugin/src/.libs/libmolfile_plugin0.a modules/cealign/src/ccealignmodule.o ov/src/.libs/libov.a layer0/.libs/liblayer0.a layer1/.libs/liblayer1.a layer2/.libs/liblayer2.a layer3/.libs/liblayer3.a
Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb.
You don't need a license for the open source version. If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. -David On Oct 4, 2012, at 9:22 PM, Mike Marchywka marchy...@hotmail.com wrote: fwiw, I never figured out why the out-of-the-box build hung using the python approach but I went through the ./cogifure, make make install route and did get the test molecules to display. However, I ran into lots of problems with the ShaderMgr and ccealignmodule and then finally the link was missing -lGLEW. In any case it looks like I am all set but I thought the download would come closer to working right away. And the xyz files I wanted to display do appear to come up just great. So do I need a license for the open source version? Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave message 989-348-4796 (P)- emergency From: marchy...@hotmail.com To: pymol-users@lists.sourceforge.net Date: Thu, 4 Oct 2012 15:43:53 -0400 Subject: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. Is there some common reason for this? CPU on one core stays at 100 percent and no more menu's come up. The larger window says at the bottom that the version is supposed to be licensed but I just pulled it down from sourceforge and not sure that this version needs a key to work. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)- leave message 989-348-4796 (P)- emergency -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-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 -- Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-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
