[PyMOL] opensource for commercial use?
Hello: I just got a question: can we use the open source version of pymol for commercial usage? Or can we develop some commercial tool based on Pymol? thank you very much. Albert -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ 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 can we rotate torsion angle of a molecule?
Hello: I am just wondering is it possible to rotate the torsion angle of a molecule in Pymol? I search in pymolwiki, and I only find how to translate a molecule or move the atom positions, but I didn't find anything about how to rotate a torsion angle of a molecule. Meanwhile, I am just wondering is it possible for pymol give alternative rotamer conformation of a protein residue? thanks a lot Albert -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ 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] problem of Pymol git install
Hello: I've installed pymol git repo following steps: http://www.pymolwiki.org/index.php/Git_install However, when I start pymol, it always showed the following messages: No module named tkintertable.Tables Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui). No module named wx Unable to initialize plugin 'mtsslTrilaterate' (pmg_tk.startup.mtsslTrilaterate). I am just wondering how can we solve the problem? thank you very much. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ 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 can we change GUI font size?
Hello: I notice that my screen resolution is too high that the font of pymol GUI looks extremely small. I am just wondering is it possible to increase them? thank you very much. -- Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ ___ 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 copy color?
Hello: I've colored object1 in various color in different regions. I am just wondering how can we copy the color scheme for object1 to object2? Object 2 is the same protein with object1 but with different conformations. Thank you very much Albert -- ___ 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] any hotkey?
Hello: I am just wondering is there any hotkey in Pymol so that we can center in the Ligand automatically? For instance: If I press keyboard "L", Pymol zoom to ligand binding pocket automatically Thanks a lot Albert -- Monitor Your Dynamic Infrastructure at Any Scale With Datadog! Get real-time metrics from all of your servers, apps and tools in one place. SourceForge users - Click here to start your Free Trial of Datadog now! http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140 ___ 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] can we show ligand in 2D?
Hello: I've got a 3D coordinate in 3D. I am just wondering is it possible to show it in 2D diagram in Pymol for a ligand so that we can get more clear idea how exactly the ligand looks like? thanks a lot Albert -- ___ 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 can we display properties?
Hello: I've got a ligand .sdf file which contains many informations such as: molecule weight, logP, surface area and so on. I am just wondering is it possible to display those properties in Pymol? Thank you very much Albert -- ___ 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] label
Hello: Does anybody have any idea whether pymol could label the absolute configuration (R/S) for a chiarity atom? Thank you very much. Albert -- Monitor Your Dynamic Infrastructure at Any Scale With Datadog! Get real-time metrics from all of your servers, apps and tools in one place. SourceForge users - Click here to start your Free Trial of Datadog now! http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140 ___ 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] APBS problem
Hello: I am trying to calculate the protein surface electstatic properities by APBS plugin in pymol. But it always failed with messages: Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx ObjectMapLoadDXFile-Error: Unable to open file! ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist? Does anybody has any idea how to solve this problem? thx a lot -- ___ 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 setup environment for APBS?
Hello: I noticed that each time when I try to use APBS plugin, pymol always ask to specify the location of: apbs psize.py pdb2pqr.py I am just wondering can we somehow write the location of those program into .pymolrc file so that each time Pymol APBS plugin can find it automatically? thanks a lot Albert -- ___ 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] APBS problem
thanks a lot for reply. Problem solved after I specify the maloc library path explicitly in my tcsh environment. setenv FETK_LIBRARY /home/albert/install/apbs/apbs-1.4.0/lib On 10/08/2015 05:02 PM, Andreas Forster wrote: Hi Albert, I apologize that I take your email for a grumpy old man's rant, but I feel this mailing list is getting washed out with poorly formulated questions. What happened to specifying what OS you use, what version of PyMOL, what version of the apbs plugin. Also, to give answers, it would help to know what settings you chose for the calculation of the electrostatic potential. There's a bunch of buttons to click. Which ones did you choose? What step have you already taken to overcome the problem? Basically, I'm asking new users to spend a leisurely coffee break reading http://www.catb.org/~esr/faqs/smart-questions.html <http://www.catb.org/%7Eesr/faqs/smart-questions.html> and then ask better question. The answer to your problem: /tmp/1-PE0.dx needs to be generated. That's all I can infer from the information you gave. All best. Andreas -- ___ 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] restriction format?
Hello: I've got a question about saving format. I've prepared a pymol section file: test.pse. I am just wondering is it possible for us to add some restriction for it? For instance: if I share this file with others, they can only visualize it in Pymol, but they don't have the permission to export them as PDB file or the like Thank you very much Albert -- ___ 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 to webGL?
Hello: I noticed that there is a plugin called exportToWeb.py I try to rum it with command: python exportToWeb.py test.pse However, no any new file generated I am just wondering how shall we use this script correctly? thanks a lot Albert -- ___ 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 to webGL?
Thanks a lot for further advice. Here is what I got: PyMOL> run exportToWeb.py PyMOL>exportToWeb my Traceback (most recent call last): File "/home/albert/install/pymol-1.7.6/modules/pymol/parser.py", line 256, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File "exportToWeb.py", line 118, in dump_rep ret += parseObjMol(obj) File "exportToWeb.py", line 50, in parseObjMol if (rep[5] == 1): TypeError: 'int' object has no attribute '__getitem__' If possible, would you please give me some suggestions? Thanks a lot Albert On 10/17/2015 04:36 PM, Osvaldo Martin wrote: Hi Albert, I do the following steps and I get a .html file as expected. 1. I download and unpack this <http://sourceforge.jp/projects/webglmol/downloads/54536/pymol-exporter-0.01.zip/> file. The script there seems to be similar to the one you attached. 2. Lauch PyMOL and do some stuff 3. cd to the folder creating during unpacking 4. run the script by doing |run exportToWeb.py | 5. then run the commnand |exportToWeb PymolObjectName | where PymolObjectName is the name of the pymol object you want to export 6. check the unpacked folder for a file with the name PymolObjectName.html Could you try to follow these steps and tell us what you get? Cheers, Osvaldo. -- ___ 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 to webGL?
Dear Osvaldo: Thanks a lot for further information. I just run the command |set pse_export_version, 1.72 | before I load anything to pymol, then followed the step for exporting. But it still failed with messages: Traceback (most recent call last): File "/home/albert/install/pymol/modules/pymol/parser.py", line 256, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File "exportToWeb.py", line 119, in dump_rep ret += parseObjMol(obj) File "exportToWeb.py", line 57, in parseObjMol if (rep[7] == 1): IndexError: list index out of range Thank you very much. -- ___ 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 enable 3D
Hello: I just notice that nowadays the webGL and xml5 technology developed so fast that many new tools emerging these days. I am really impressed by the GLMOL tool for pymol recently. It is really powerful. I am just wondering is it possible to enable anaglyph or side by side stereo for GLMOL tool? I just find a a tool based in GLmol, called iview which support such kind of function. Is it possible for the developer integrate them into GLmol python script so that the generated .html file can also support some simple stereo view? Here is the link of website: http://istar.cse.cuhk.edu.hk/iview/ and here is script for this tool https://github.com/HongjianLi/istar/tree/master/public/iview Thank you very much. Albert -- ___ 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] GTX980Ti for Pymol 3D?
Hello: Does anybody know whether Nvidia GTX980Ti support Pymol active stereo 3D? I saw someone said that some GTX graphic card may also work, but I am not sure for this one. Thx a lot -- ___ 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] Stacking Interactions
I think the major concern is how Pymol depicts the pi-pi stacking Of course we can identify such interaction immediately as soon as we open the system in Pymol. However there is no any components to indicate this, eg: we can depict the H-bond with a dash between two atoms but how could pi-pi interaction be depicted? On 11/10/2015 07:03 AM, Osvaldo Martin wrote: Hi Amali, I am not aware that PyMOL has this feature implemented out-of-the-box. Nevertheless this can be done with PyMOL. A crude approximation will be to measure the distance between the center of aromatic rings and consider a pi-pi stacking for distances shorter than a threshold value. A better model will probably include a distance threshold and one or two angles in the definition. Are you trying to estimate pi-pi stacking interactions in general or for a particular system? Cheers, Osvaldo. -- ___ 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] problem of pymol 1.8
Hello: I've installed the open source code version pymol 1.8 in my Linux OS. However, when I start pymol, it always showed the following messages: No module named tkintertable.Tables Unable to initialize plugin 'mtsslDockGui' (pmg_tk.startup.mtsslDockGui). No module named wx Unable to initialize plugin 'mtsslTrilaterate' (pmg_tk.startup.mtsslTrilaterate). I am just wondering how can we solve the problem? I've already installed python PMW in my machine. thank you very much. Albert -- ___ 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] problem of pymol 1.8
Hi Thomas: thanks a lot for helpful advice. HOwever, I got something new warnings: No module named cPluginManager Unable to initialize plugin 'xPyder' (pmg_tk.startup.xPyder). No module named backend_wxagg Unable to initialize plugin 'mtsslPlotter' (pmg_tk.startup.mtsslPlotter). I google it, and cannot find any helpful information.... thanks again ALbert On 11/18/2015 11:16 PM, Thomas Holder wrote: > Hi Albert, > > These messages come from third-party plugins that you have installed, see: > http://pymolwiki.org/index.php/MtsslDock > http://pymolwiki.org/index.php/MtsslTrilaterate > > Cheers, >Thomas -- ___ 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] default fetch format
Hello: I noticed that if we run command: fetch 2ac1 to get PDB into pymol in Version 1.8.0, it downloaded .cif file by default. I am just wondering is it possible to change the default format as .pdb file? thanks a lot Albert -- ___ 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] can we clone representation?
Hello: I've shown an object as cartoon and displaced sticks with various colors. I am just wondering, can we clone all representation from object 1 to object 2 with some command in Pymol? As far as I known, this is possible in VMD: http://www.ks.uiuc.edu/Research/vmd/plugins/clonerep/ Thank you very much Albert -- ___ 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] default fetch format
Hi Thomas:
thanks a lot for helpful advice.
May I ask is there any superior features of mmCIF format against PDB format?
regards
Albert
On 11/22/2015 04:15 PM, Thomas Holder wrote:
> Hi Albert,
>
> Unfortunately the default fetch type can't be configured. But you can
> override the fetch command. Example which you could place in your ~/.pymolrc
> file:
>
> python
> from pymol import cmd
>
> def fetchpdb(*args, **kwargs):
> if 'type' not in kwargs:
> kwargs['type'] = 'pdb'
> return cmd.fetch(*args, **kwargs)
>
> cmd.extend('fetch', fetchpdb)
> python end
>
> However, if you don't have a compelling reason to work with PDB instead of
> mmCIF, then I recommend to give the new mmCIF default a try.
>
> Cheers,
--
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[PyMOL] real time minization in Pymol
Hello: I just found a a very nice module of pymol, called "Molecular Sculpting". However, according to the description in Pymolwiki, it works like a real-time energy minimizer, except that it isn't minimizing the energy. Instead, its just trying to return local atomic geometries (bonds, angles, chirality, planarity) to the configuration the molecules possess when they were first loaded into PyMOL. So I am just wondering does the developer have any planning to improve this nice too? For instance introducing forcefiled for this tool (eg: Amber FF for protein, GAFF for the ligand). There is a "optimize" plugin in Pymol, maybe the developer can consider merge them together? Thank you very much Albert -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 ___ 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] real time minization in Pymol
Yes, I also really love this function. However, for the sake of accuracy, I believe many users will also strongly demand for introducing forcefield for minimization..I am looking forward to see that "optimize" plugin would somehow merged into "Molecular Sculpting".At least, it is very easy and free to get access to Amber and GAFF forcefield. Thanks again. On 11/23/2015 05:07 PM, H. Adam Steinberg wrote: > I would love to see this feature improved! > > Try it out if you have never used it. It works quite well. It is quite > processor intensive and it can take over your computer when it is running…. I > have also found when you uncheck it in the menu, it will still continue to > run and I end up force quitting to get it to stop. -- Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 ___ 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] how to close displaying a molecule
just click the b.pdb on the Pymol object manager bar to undisplay it. That's the basic of basic usage of Pymol. Wouldn't it be nice if you spend a few minutes to go through Pymol manual? On 12/11/2015 08:19 AM, Smith Liu wrote: Dear All, Suppose by pymol I have opened A.pdb abd B.pdb. Is anyway I close B.pdb and have only A.pdb displayed? Smith -- ___ 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 crashed reading any structure file
Dear: I've compiled pymol-1.8.0 under my Linux X64 OS. I found that Pymol can start by command: pymol without any complaints or erros. However, when I try to load a .pdb file into pymol, pymol always failed with following messages: --- stephen@linux:~/tmp> pymol 4eiy.pdb PyMOL(TM) Molecular Graphics System, Version 1.8.0.0. Copyright (c) Schrodinger, LLC. All Rights Reserved. Created by Warren L. DeLano, Ph.D. PyMOL is user-supported open-source software. Although some versions are freely available, PyMOL is not in the public domain. If PyMOL is helpful in your work or study, then please volunteer support for our ongoing efforts to create open and affordable scientific software by purchasing a PyMOL Maintenance and/or Support subscription. More information can be found at "http://www.pymol.org";. Enter "help" for a list of commands. Enter "help " for information on a specific command. Hit ESC anytime to toggle between text and graphics. Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.30. OpenGL graphics engine: GL_VENDOR: VMware, Inc. GL_RENDERER: Gallium 0.4 on llvmpipe (LLVM 3.4, 256 bits) GL_VERSION: 2.1 Mesa 10.0.3 Detected 4 CPU cores. Enabled multithreaded rendering. HEADERMEMBRANE PROTEIN06-APR-12 4EIY TITLE CRYSTAL STRUCTURE OF THE CHIMERIC PROTEIN OF A2AAR-BRIL IN COMPLEX TITLE2 WITH ZM241385 AT 1.8A RESOLUTION COMPNDMOL_ID: 1; COMPND 2 MOLECULE: ADENOSINE RECEPTOR A2A/SOLUBLE CYTOCHROME B562 CHIMERA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME B-562; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES ObjectMolecule: Read secondary structure assignments. ObjectMolecule: Read crystal symmetry information. CmdLoad: "4eiy.pdb" loaded as "4eiy". /home/stephen/install/pymol-1.8.0/pymol: line 3: 10490 Segmentation fault "/usr/bin/python" "/home/stephen/install/pymol-1.8.0/modules/pymol/__init__.py" "$@" - I am just wondering what's the problem? I also tried .cif, .mol2 files, and all of them failed. thx a lot -- ___ 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 get an atom coordinates information
Hello: I would like to know the XYZ information of a specific atom. I am just wondering how can we do this? Is there any command line? thank you very much Albert -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 ___ 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] why lib/python folder is missing?
Hello: I am using the following command line to compile PYmol: setenv prefix /home/albert/install/pymol/open-1.8 setenv modules $prefix/modules python setup.py build install --home=$prefix --install-lib=$modules --install-scripts=$prefix However, I noticed that there is no the "lib/python2.7" folder in the installation directory.. normally this should be placed in : /home/albert/install/pymol/open-1.8/ext/lib/python2.7 I am just wondering how can we fix this problem? thanks a lot -- ___ 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] VR for Pymol?
Hello: Does anybody have any idea whether PyMol support Virtual Reality (VR)? Can we use the following VR devices to visualize PyMOl in computer? http://www.polygon.com/2016/1/5/10719326/nvidia-virtual-reality-performance-power https://www.youtube.com/watch?v=U4JPhUr_d7g If yes, will any VR device on the market work for PyMol? Thanks a lot -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports. http://sdm.link/zohomanageengine ___ 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 hide dashed artificial cartoon?
Hello: I noticed that if I show my structure as cartoon, there would be a "dashed loop" cartoon filling in the missing part of my structure. I am just wondering how can we disable PyMol show the missing part automatically? Thank you very much Albert -- ___ 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] problem of internal_gui
Hello: I used commad line: set internal_gui, off to hide the internal gui. Then I save my pymol session as a .pse file. However, when I reopen this .pse file, the internal_gui is still there. When I insert .pse file to a PPT file, the internal_gui is also there. I am just wondering how to solve this problem? I am using PyMOL-1.8.2.3. I also tested in the latest 1.8.4, it has the same issue. Thank you very much. Albert -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ 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] problem of internal_gui
I see. It works very well now. Thanks a lot On 10/06/2016 10:32 PM, Thomas Holder wrote: > Hi Albert, > > "internal_gui" is now a blacklisted setting not be stored or restored from > session files. > > You can launch PyMOL without internal gui like this from a Terminal: > > pymol -i session.pse > > When inserting in AxPyMOL, please check the option > > [x] PyMOL Show (Hide controls) > > For older versions of AxPyMOL (before 1.7 I think) the session needs to be > saved as a "PyMOL Show file" (with .psw Extension) to be loaded without > controls into AxPyMOL. > > Hope that helps. > > Cheers, >Thomas -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ 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] problem of optirun in Pymol
Hello: I've got 2 graphic card in my laptop: Intel® HD Graphics 4600+ Nvidia M1100M I have installed Bumblee optirun in my Linux OS. Currently, command line optirun pymol works fine for Pymol-1.8.2.3. However, I found that it doesn't work for Pymol-1.8.4. When I type optirun pymol Pymol doesn't start and I didn't get any error messages from terminal either. I am just wondering how can we solve the problem? Thx a lot Albert -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ 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] problem of optirun in Pymol
Hello: I am using openSUSE 13.2 X64 OS. Pymol works fine without optirun in 1.8.4. Here is output from ./pymol -c PyMOL>python end PyMOL: normal program termination. However, when I type optirun ./pymol -c I didn't obtain any information. regards Albert On 10/10/2016 08:46 PM, Thomas Holder wrote: > Hi Albert, > > Which Linux OS and version (e.g. Ubuntu 12.04 64bit) is this? > Does PyMOL work without optirun? > Does it work in headless mode (pymol -c)? > > Thanks, >Thomas -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ 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 show PBC box?
Hello: I am visualizing a MD simulation system in PyMOL. It contains the PBC information. I am just wondering how can we show the PBC box in PyMOL? As far as I know the PBC box can be shown in VMD using the following command line: >pbc box Is there any similar command line in PyMOL? Thank you very much. Albert -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/xeonphi ___ 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] how to show PBC box?
Dear Tsjerk: Thanks a lot for such prompt reply. It works very well. Cheers. Albert On 12/07/2016 08:46 PM, Tsjerk Wassenaar wrote: Hi Albert, You can do: show cell Cheers, Tsjerk -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/xeonphi___ 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] Save command output to a file in pymol
I think you can obtain it from your Linux terminal On 01/13/2017 10:34 AM, Academic Research wrote: Pymol Professionals I need your help, I have the following command: |iterate n. CA, print resi + ':' + ss | I use this command in pymol to print out each residue number and its corresponding secondary structure. The command prints out the result in pymol itself. My question is: *How can I save the output from this command into a file?* AC Research -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi___ 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] New plugin: PyMOLProbity
fantastic job!! Thanks a lot. Albert On 01/16/2017 10:16 PM, Sampson, Jared M. wrote: Dear PyMOL Users, I am pleased to introduce a new plugin called PyMOLProbity <https://github.com/jaredsampson/pymolprobity> which allows a PyMOL user to visualize MolProbity-style structural validation data directly in a PyMOL session. The programs Reduce, Flipkin, and Probe from the well-known MolProbity <http://molprobity.biochem.duke.edu/> software package allow generation of data in "kinemage" (kinetic image) format to illustrate atom-atom contacts (dots) and clashes (spikes), and the new plugin now makes it possible to utilize the same programs to produce similar results in PyMOL scenes. I have put together a page on the PyMOL Wiki <https://pymolwiki.org/index.php/PyMOLProbity> with a brief summary of its features and basic how-to information. (Please note that the MolProbity executables are only available for Linux/MacOS, so PyMOLProbity isn't yet useful on Windows.) My work on this plugin was supported by the Warren L. DeLano Memorial PyMOL Open-Source Fellowship. I would like once again to thank Schrödinger for the opportunity to work on this project, and in particular would like to thank the PyMOL developers for their support and feedback along the way. I hope many of you will find it useful. If you come across any bugs or have any feature requests or other suggestions, please feel free to email me directly or create a new issue <https://github.com/jaredsampson/pymolprobity/issues> on Github. Happy PyMOLing! Cheers, Jared -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot___ 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 convert .pse to html?
Hello, I've got a pymol .pse file and I am just wondering how can we convert it with a Linux command line directly to a .html file without opening pymol GUI? Thank you very much. Albert -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ 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] how to convert .pse to html?
Hi Thomas, Thanks a lot for your information. I know this command and that's what I needed. However, I don't what to open the PyMOL GUI. Is it possible that we run PyMOL with a text mode and convert the .pse file directly to a .html file? Thanks again. Albert On 01/25/2017 10:46 PM, Thomas Holder wrote: > Hi Albert, > > What kind of HTML content do you expect? A page with a PNG image? Or an > interactive 3D model? Check out > this:https://pymolwiki.org/index.php/Pymol2glmol > > Cheers, >Thomas -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ 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] how to convert .pse to html?
BTW, I try to run the example command line, but it always failed with messages: PyMOL>pymol2glmol 1tqn Traceback (most recent call last): File "/usr/lib64/python2.7/site-packages/pymol/parser.py", line 256, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File "/home/albert/install/pymol/Pymol-script-repo/pymol2glmol.py", line 152, in dump_rep int(255 * float(bgcolor[1])), int(255 * float(bgcolor[2]))) IndexError: tuple index out of range Do you have any idea what's the problem? THX again. On 01/25/2017 10:46 PM, Thomas Holder wrote: > Hi Albert, > > What kind of HTML content do you expect? A page with a PNG image? Or an > interactive 3D model? Check out > this:https://pymolwiki.org/index.php/Pymol2glmol > > Cheers, >Thomas -- Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot ___ 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] unable to export obj
Hi, I am trying to get a .obj file, but fail when setting up surface_type to 2. More explicitly: > load 1ppe.pdb, 1ppe > set surface_type, 2 > hide everything > show surface shows a nice triangulated surface. However, > save myscene.obj saves an empty file. I've tried pymol versions 1.7.4 and 1.6.0. Saving into an obj file works well when surface_type is set to 0, or 1. Any help? Best, Albert -- ----- Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds -- New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet ___ 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] RMS over a MD trajectory.
Hi, I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I can see that "align" does things correctly when: align trj, pdb1, mobile_state=1 i. e., when I align the first snapshot of the trajectory with the PDB file. I also understand that PyMOL does compute the RMS along the trajectory if I simply: align trj, pdb1 as it is told in: http://www.pymolwiki.org/index.php/Align However, I am unable to get the list of RMS values printed out. How could I do that? Thanks, Albert -- ----- Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ 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] RMS over a MD trajectory.
Terribly useful Carsten!
I could easily do a loop and get the RMS along the trajectory:
k = []
for i in range(1,101): k.append(cmd.align("trj","pdb1",mobile_state=i))
for i in range(100): print k[i][0]
Cheers,
Albert
On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
> Hi Al,
>
> you would need to go through the Python API:
>
> python
> rms=cmd.align("mobCA","tarCA", quiet=0)
> print rms
> python end
>
> rms contains a tuple with various parameters related to the superposition.
> The first value in the tuple i.e. rms[0] should be the RMS value.
>
> HTH
>
> Carsten
>
> -Original Message-
> From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
> Sent: Wednesday, May 06, 2015 8:32 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] RMS over a MD trajectory.
>
> Hi,
> I am trying to compute the RMS between a PDB file and a Gromacs trajectory. I
> can see that "align" does things correctly when:
>align trj, pdb1, mobile_state=1
> i. e., when I align the first snapshot of the trajectory with the PDB file. I
> also understand that PyMOL does compute the RMS along the trajectory if I
> simply:
>align trj, pdb1
> as it is told in:
> http://www.pymolwiki.org/index.php/Align
> However, I am unable to get the list of RMS values printed out. How could I
> do that?
>
> Thanks,
> Albert
>
> --
> -
> Dr Albert Solernou
> EPSRC Research Fellow,
> Department of Physics and Astronomy,
> University of Leeds
> Tel: +44 (0)1133 431451
>
>
> --
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> ___
> 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
--
-
Dr Albert Solernou
EPSRC Research Fellow,
Department of Physics and Astronomy,
University of Leeds
Tel: +44 (0)1133 431451
--
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
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Re: [PyMOL] RMS over a MD trajectory.
Thanks Thomas,
I was already printing k[i][3] (RMSD before refinement) instead of
k[i][0] (RMSD after refinement) but your "cycles=0" looks cleaner.
Cheers,
Albert
On 05/06/2015 05:14 PM, Thomas Holder wrote:
> Hi Albert,
>
> Please pay attention to the difference between all-atom RMSD and RMSD after
> outlier rejection.
> http://pymolwiki.org/index.php/Align#RMSD
>
> If your "trj" and "pdb1" have identical topology and matching atom
> identifiers, then you can also use cmd.rms().
> http://pymolwiki.org/index.php/Rms
>
> Cheers,
>Thomas
>
> On 06 May 2015, at 11:56, Albert Solernou wrote:
>
>> Terribly useful Carsten!
>>
>> I could easily do a loop and get the RMS along the trajectory:
>> k = []
>> for i in range(1,101): k.append(cmd.align("trj","pdb1",mobile_state=i))
>> for i in range(100): print k[i][0]
>>
>> Cheers,
>> Albert
>>
>>
>> On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
>>> Hi Al,
>>>
>>> you would need to go through the Python API:
>>>
>>> python
>>> rms=cmd.align("mobCA","tarCA", quiet=0)
>>> print rms
>>> python end
>>>
>>> rms contains a tuple with various parameters related to the superposition.
>>> The first value in the tuple i.e. rms[0] should be the RMS value.
>>>
>>> HTH
>>>
>>> Carsten
>>>
>>> -Original Message-
>>> From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
>>> Sent: Wednesday, May 06, 2015 8:32 AM
>>> To: pymol-users@lists.sourceforge.net
>>> Subject: [PyMOL] RMS over a MD trajectory.
>>>
>>> Hi,
>>> I am trying to compute the RMS between a PDB file and a Gromacs trajectory.
>>> I can see that "align" does things correctly when:
>>>align trj, pdb1, mobile_state=1
>>> i. e., when I align the first snapshot of the trajectory with the PDB file.
>>> I also understand that PyMOL does compute the RMS along the trajectory if I
>>> simply:
>>> align trj, pdb1
>>> as it is told in:
>>>http://www.pymolwiki.org/index.php/Align
>>> However, I am unable to get the list of RMS values printed out. How could I
>>> do that?
>>>
>>> Thanks,
>>> Albert
>>>
>>> --
>>> -
>>> Dr Albert Solernou
>>> EPSRC Research Fellow,
>>> Department of Physics and Astronomy,
>>> University of Leeds
>>> Tel: +44 (0)1133 431451
--
-
Dr Albert Solernou
EPSRC Research Fellow,
Department of Physics and Astronomy,
University of Leeds
Tel: +44 (0)1133 431451
--
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
___
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Re: [PyMOL] RMS over a MD trajectory.
Oh, I see...
It looks like I'll need to end up writing a short script that does the
loop along the trajectory together with a correct RMS calculation.
Thanks for the tip, Carsten.
Cheers,
Albert
On 05/08/2015 04:11 PM, Schubert, Carsten [JRDUS] wrote:
> Hi Al,
>
> based on my experience running align or super with "cycles=0" has the
> tendency to produce inferior alignment results. So depending on how similar
> the conformation of your structures are you may end up with skewed
> statistics. What I've done in the past and for a paper I'm working on now is
> to run the alignment with default parameters to get the best superposition
> and then calculate the statistics by hand from the superposed structures. Not
> sure if cmd.rms() would do this for all residues w/o outlier rejection, so I
> ended up writing code for myself. The colorbyrmsd.py
> (http://pymolwiki.org/index.php/ColorByRMSD) script gives a nice illustration
> on how to approach this this.
>
> Carsten
>
> -Original Message-
> From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
> Sent: Friday, May 08, 2015 10:04 AM
> To: Thomas Holder
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] RMS over a MD trajectory.
>
> Thanks Thomas,
> I was already printing k[i][3] (RMSD before refinement) instead of k[i][0]
> (RMSD after refinement) but your "cycles=0" looks cleaner.
>
> Cheers,
> Albert
>
> On 05/06/2015 05:14 PM, Thomas Holder wrote:
>> Hi Albert,
>>
>> Please pay attention to the difference between all-atom RMSD and RMSD after
>> outlier rejection.
>> http://pymolwiki.org/index.php/Align#RMSD
>>
>> If your "trj" and "pdb1" have identical topology and matching atom
>> identifiers, then you can also use cmd.rms().
>> http://pymolwiki.org/index.php/Rms
>>
>> Cheers,
>> Thomas
>>
>> On 06 May 2015, at 11:56, Albert Solernou wrote:
>>
>>> Terribly useful Carsten!
>>>
>>> I could easily do a loop and get the RMS along the trajectory:
>>>k = []
>>>for i in range(1,101): k.append(cmd.align("trj","pdb1",mobile_state=i))
>>>for i in range(100): print k[i][0]
>>>
>>> Cheers,
>>> Albert
>>>
>>>
>>> On 05/06/2015 04:20 PM, Schubert, Carsten [JRDUS] wrote:
>>>> Hi Al,
>>>>
>>>> you would need to go through the Python API:
>>>>
>>>> python
>>>> rms=cmd.align("mobCA","tarCA", quiet=0) print rms python end
>>>>
>>>> rms contains a tuple with various parameters related to the superposition.
>>>> The first value in the tuple i.e. rms[0] should be the RMS value.
>>>>
>>>> HTH
>>>>
>>>>Carsten
>>>>
>>>> -Original Message-
>>>> From: Albert Solernou [mailto:a.soler...@leeds.ac.uk]
>>>> Sent: Wednesday, May 06, 2015 8:32 AM
>>>> To: pymol-users@lists.sourceforge.net
>>>> Subject: [PyMOL] RMS over a MD trajectory.
>>>>
>>>> Hi,
>>>> I am trying to compute the RMS between a PDB file and a Gromacs
>>>> trajectory. I can see that "align" does things correctly when:
>>>> align trj, pdb1, mobile_state=1
>>>> i. e., when I align the first snapshot of the trajectory with the PDB
>>>> file. I also understand that PyMOL does compute the RMS along the
>>>> trajectory if I simply:
>>>> align trj, pdb1
>>>> as it is told in:
>>>> http://www.pymolwiki.org/index.php/Align
>>>> However, I am unable to get the list of RMS values printed out. How could
>>>> I do that?
>>>>
>>>> Thanks,
>>>> Albert
>>>>
>>>> --
>>>> -
>>>> Dr Albert Solernou
>>>> EPSRC Research Fellow,
>>>> Department of Physics and Astronomy,
>>>> University of Leeds
>>>> Tel: +44 (0)1133 431451
> --
> -
> Dr Albert Solernou
> EPSRC Research Fellow,
> Department of Physics and Astronomy,
> University of Leeds
> Tel: +44 (0)1133 431451
>
>
> --
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and
[PyMOL] rms_cur, rms, fit - No atoms selected
I'm new at pymol, and I'm trying to use the commands rms and rms_cur. I have two pdb files, with two proteins in each. First, I load the files > load 1acb_321000.pdb, c321 > load 1acb_dock.pdb, dock then I select the backbone of the B chain of each complex, > select lc, /c321//b//ca+c+n+o > select lr, /dock//b//ca+c+n+o Everything works until here. Each selection is showed on the screen, and they are 207 atoms each. Now I want to get the rms value without superimposing: > rms_cur lc, lr but it does not work: ExecutiveRMS-Error: No atoms selected. It also does not work with rms or fit commands, although it works with align: > align lc, lr Match: read scoring matrix. Match: assigning 69 x 69 pairwise scores. MatchAlign: aligning residues (69 vs 69)... ExecutiveAlign: 207 atoms aligned. ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=0.01). ExecutiveRMS: 2 atoms rejected during cycle 2 (RMS=0.01). Executive: RMS =0.006 (200 to 200 atoms) I've seen that someone has reported a bug at debian's, under the version 0.99rc6: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=486254 I've tried the 1.0r2-1 version (commming with ubuntu, apt-get), and compliling the source code from the svn of the current version, 1.2-x. Same results. Hope someone can help me, albert
Re: [PyMOL] rms_cur, rms, fit - No atoms selected
Thanks!! Now it works!! albert En/na Warren DeLano ha escrit: > (Sorry if this is dupe -- my email client is acting up...) > > the rms_* and fit commands required that the atoms in each selection to have > matching identifiers: such as chain, resi, segi, resn, etc. You can use the > "alter" command to set the identifiers to matching values before issuing such > commands: > > alter all, segi='' > > alter c321 and chain E, chain='A' > > alter c321 and chain I, chain='B' > > etc. > > Cheers, > Warren > > > > From: Albert Solernou [mailto:alb...@mmb.pcb.ub.es] > Sent: Thu 4/23/2009 9:42 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] rms_cur, rms, fit - No atoms selected > > > > I'm new at pymol, and I'm trying to use the commands rms and rms_cur. > > I have two pdb files, with two proteins in each. > First, I load the files > >> load 1acb_321000.pdb, c321 >> load 1acb_dock.pdb, dock > > then I select the backbone of the B chain of each complex, >> select lc, /c321//b//ca+c+n+o >> select lr, /dock//b//ca+c+n+o > > Everything works until here. Each selection is showed on the screen, and > they are 207 atoms each. Now I want to get the rms value without > superimposing: > >> rms_cur lc, lr > > but it does not work: > ExecutiveRMS-Error: No atoms selected. > It also does not work with rms or fit commands, although it works with > align: > >> align lc, lr > Match: read scoring matrix. > Match: assigning 69 x 69 pairwise scores. > MatchAlign: aligning residues (69 vs 69)... > ExecutiveAlign: 207 atoms aligned. > ExecutiveRMS: 5 atoms rejected during cycle 1 (RMS=0.01). > ExecutiveRMS: 2 atoms rejected during cycle 2 (RMS=0.01). > Executive: RMS =0.006 (200 to 200 atoms) > > > I've seen that someone has reported a bug at debian's, under the version > 0.99rc6: > > http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=486254 > > > I've tried the 1.0r2-1 version (commming with ubuntu, apt-get), and > compliling the source code from the svn of the current version, 1.2-x. > Same results. > > Hope someone can help me, > albert > > -- > Stay on top of everything new and different, both inside and > around Java (TM) technology - register by April 22, and save > $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. > 300 plus technical and hands-on sessions. Register today. > Use priority code J9JMT32. http://p.sf.net/sfu/p > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensign option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] selecting faces and vertices in CGOs
Dear All, I was wondering if there is a way to select faces, vertices and/or edges from a CGO either using the mouse or the command line. How difficult would be to add this, and how would you do that? It would be very useful for us if we could get that working. Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140 ___ 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] selecting faces and vertices in CGOs
Hi Thomas, thanks for your answer. Even if it is challenging, I could still be interested in coding that. I have written a plugin for PyMOL that we plan to release as soon as it proves to be stable, together with another piece of software, and that functionality would help us very much. I would be very grateful if you could give me some hints on the code structure, and on how to tackle the inclusion of this new feature. Cheers, Albert On 04/08/2016 09:18 PM, Thomas Holder wrote: > Hi Albert, > > This is currently not possible and adding this would be a very major project. > > Cheers, > Thomas > > On 30 Mar 2016, at 10:40, Albert Solernou wrote: > >> Dear All, >> I was wondering if there is a way to select faces, vertices and/or edges >> from a CGO either using the mouse or the command line. How difficult >> would be to add this, and how would you do that? >> >> It would be very useful for us if we could get that working. >> >> Thanks, >> Albert >> >> -- >> - >> Dr Albert Solernou >> EPSRC Research Fellow, >> Department of Physics and Astronomy, >> University of Leeds >> Tel: +44 (0)1133 431451 > -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Find and fix application performance issues faster with Applications Manager Applications Manager provides deep performance insights into multiple tiers of your business applications. It resolves application problems quickly and reduces your MTTR. Get your free trial! https://ad.doubleclick.net/ddm/clk/302982198;130105516;z ___ 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] loading StringIO
Dear All, I was wondering if there was a way to load a PDB file stored in memory instead of disk, i. e., a memory file, defined through StringIO or tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could handle an open file instead of a file? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik ___ 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] loading StringIO
Hi Jordan, I still don't figure out how to do that with "load_object". What is the "type" for a file handler? Would be "object" the file handler itself? Albert On 10/26/2016 10:58 AM, Jordan Willis wrote: > Probably could use load_object instead. > > >def load_object(type,object,name,state=0,finish=1,discrete=0, > quiet=1,zoom=-1,_self=cmd): > ''' > DESCRIPTION > > "load_object" is a general developer function for loading Python objects > into PyMOL. >> On Oct 26, 2016, at 1:55 AM, Albert Solernou > <mailto:a.soler...@leeds.ac.uk>> wrote: >> >> Dear All, >> I was wondering if there was a way to load a PDB file stored in memory >> instead of disk, i. e., a memory file, defined through StringIO or >> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could >> handle an open file instead of a file? >> >> Thanks, >> Albert >> >> >> -- >> - >> Dr Albert Solernou >> EPSRC Research Fellow, >> Department of Physics and Astronomy, >> University of Leeds >> Tel: +44 (0)1133 431451 >> >> -- >> The Command Line: Reinvented for Modern Developers >> Did the resurgence of CLI tooling catch you by surprise? >> Reconnect with the command line and become more productive. >> Learn the new .NET and ASP.NET <http://ASP.NET> CLI. Get your free copy! >> http://sdm.link/telerik >> _______ >> 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 > -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik ___ 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] loading StringIO
That's lovely, David. Thanks, Albert On 10/26/2016 11:56 AM, David Hall wrote: > https://pymolwiki.org/index.php/Read_Pdbstr > > -David > > On Oct 26, 2016, at 3:55 AM, Albert Solernou <mailto:a.soler...@leeds.ac.uk>> wrote: > >> Dear All, >> I was wondering if there was a way to load a PDB file stored in memory >> instead of disk, i. e., a memory file, defined through StringIO or >> tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could >> handle an open file instead of a file? >> >> Thanks, >> Albert >> >> >> -- >> - >> Dr Albert Solernou >> EPSRC Research Fellow, >> Department of Physics and Astronomy, >> University of Leeds >> Tel: +44 (0)1133 431451 >> >> -- >> The Command Line: Reinvented for Modern Developers >> Did the resurgence of CLI tooling catch you by surprise? >> Reconnect with the command line and become more productive. >> Learn the new .NET and ASP.NET <http://ASP.NET> CLI. Get your free copy! >> http://sdm.link/telerik >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net >> <mailto: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 -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik ___ 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] sources for PyMOL 2
Dear All, we have been writing a plugin for PyMOL during the last years, released as GPL. I would like to support PyMOL2, but need to know whether the code will be made accessible or not. Is PyMOL2 still free software? And if so, can we get access to the source code? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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] sources for PyMOL 2
OK, I found the answer myself, googling in this email list. Sources will be released early next year, I understood. I'll wait patiently :) Cheers, Albert On 22/11/17 11:49, Albert Solernou wrote: Dear All, we have been writing a plugin for PyMOL during the last years, released as GPL. I would like to support PyMOL2, but need to know whether the code will be made accessible or not. Is PyMOL2 still free software? And if so, can we get access to the source code? Thanks, Albert -- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ 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
