Re: [PyMOL] scenes and states
Hi Bob, it's the object-level state setting: fetch 1nmr 1d7q, async=0 set state, 3, 1nmr set state, 10, 1d7q And since scenes do not store settings, this cannot be stored with a scene. Cheers, Thomas On Jun 3, 2013, at 10:41 AM, Robert Hanson hans...@stolaf.edu wrote: [[sorry -- not used to a list that requires reply-all to go back to the list]] What you describe there is a way to load a specific file into a specific state, I think. I meant, once you have a set of multi-state objects, can I select to compare two different states, one from one and one from the other? 1cdr2/10 1sq35/30 and then could I make a scene that does that? -- without viewing all states Bob On Mon, Jun 3, 2013 at 9:07 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Bob, The answer is yes to all. fetch 1ubq, state=3 fetch 6lzm, state=10 cmd.load_cgo([7.0,0,0,0,2],name=sphere,state=2) The representations (e.g. surface) do have states in the sense that the each state gives a different surface. But whether the surface is shown or not is controlled globally. It is not possible to have the surface representation only in one state, such that looping over the states, the surface would suddenly pop up for one. Hope it helps, Tsjerk On Mon, Jun 3, 2013 at 2:38 PM, Robert Hanson hans...@stolaf.edu wrote: Questions: Can two objects be in two different states -- object1 in state 3 and object2 in state 10, for instance, at the same time? If so, how is that set up? How is that then incorporated into a scene? Do CGO, measurements, mesh, and volume objects have states as well? Bob -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ 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] defer_builds_mode
Hi Daniel, this memory leak is fixed in PyMOL 1.6 (latest open-source). Cheers, Thomas Daniel Mann wrote, On 05/23/13 17:56: Hello, I just wanted to leave a short note on a possible bug I've observed. When I stop PyMOL from caching the geometry of my trajectory in RAM by set_defer_builds_mode, 3 and load a rather short trajectory (ca. 100 frames) of a protein that is shown in Cartoon-representation PyMOL starts eating my RAM gradually. As the trajectory loops several times more and more is stored to RAM, even worse the reinit command doesn't get rid of the cache, whatever is cached to RAM there... This doesn't seem to happen in lines-representation, but also for sticks. (PyMOL 1.5.0.4, Ubuntu 12.04 64-bit) Regards, Daniel -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may ___ 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] Label by selection identifier
Hi Jordan, use the first operator: PyMOL label first foo, foo or for the first CA atom in foo: PyMOL label first (foo and guide), foo Cheers, Thomas Jordan Willis wrote, On 05/21/13 11:07: Yes thank you! I meant to post that as my solution considering it works pretty good. It preserves depth and position. Jordan On May 21, 2013, at 3:45 AM, Folmer Fredslund wrote: Hi Jordan, As a workaround you can label just the CA's (so this doesn't answer your question exactly, but might be usefull): label foo and n. CA, foo Hope this helps, Folmer 2013/5/21 Jordan Willis Hello, This should be straightforward, Is it possible to label selections by their name? If I have a selection named foo and I say label foo, foo, it of course labels all the atoms. Is it possible to get one label for the entire selection without using pseudoatoms? Jordan -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may ___ 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 install Psico module for pymol with window 7
Hi Stephane, psico requires python 2.6 or 2.7. I also made a python 2.5 backport [1]. But PyMOL 0.99rc6 is way too old, it ships with python 2.3. [1] https://github.com/speleo3/pymol-psico/tree/backport Cheers, Thomas On May 10, 2013, at 8:20 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello I have downloaded the Psico module of T. Holder to use the command supercell. I have followed the wiki http://www.pymolwiki.org/index.php/Psico and https://github.com/speleo3/pymol-psico/. I did the followings: 1) Installed the ccbtx and numpy librairies 2) Dowloaded the Psico archive from https://github.com/speleo3/pymol-psico/ 3) Copied the Psico directory in my C:\Program Files (x86)\DeLano Scientific\PyMOL\modules\psico 4) Lauched pymol (0.99rc6) and typed import import psico.fullinit But i obtain the following error File C:\Program Files (x86)\DeLano Scientific\PyMOL/modules\psico\fullinit.py, line 10 from . import init ^ SyntaxError: invalid syntax What's wrong ? Thanks for your help Stephane -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ 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] Secondary structure labeling
Hi Bishwa, can you be more precise what you mean by label? If the secondary structure is defined in the header of your PDB file, PyMOL can show cartoon representation, show text labels on C-alpha atoms and color by secondary structure. PyMOL as cartoon PyMOL label name CA, ss PyMOL color red, ss H PyMOL color yellow, ss S Cheers, Thomas Bishwa Subedi wrote, On 05/08/13 13:33: Hi All, I am using Pymol to make figures for my publication. I am not sure if there has been a discussion earlier but I would like to know how we can label the secondary structures (helices and strands) using Pymol. I have them defined in my header file using DSSP. Thank you in advance. Bishwa Subedi -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ 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 error
Dear Rhitankar, I should point out that Schrödinger also sells pre-compiled PyMOL with easy to use installers. http://pymol.org/academic.html Open-Source PyMOL was always targeted to power-users who are familiar with compiling software themselves. Regarding your question: It will most likely not be possible to compile and install open-source PyMOL with the system python on Mac, because OSX ships with an incompatible Tkinter library. So Pmw won't be your last problem. With macports it should work fine if you do this (see also David's answers): sudo port install tcl -corefoundation +threads sudo port install tk -quartz +x11 sudo port install pymol Hope that helps. Cheers, Thomas Rhitankar Pal wrote, On 05/08/13 18:01: Dear Thomas, Even after I installed the Pmw1.3 which should be compatible with python2.7 and reinstalling the pymol, I am still the following error message. File /Library/Python/2.7/site-packages/pymol/__init__.py, line 450, in launch_gui __import__(self.invocation.options.gui) File /Library/Python/2.7/site-packages/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 33, in module class PMGApp(Pmw.MegaWidget): File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py, line 131, in __getattr__ self._initialise() File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py, line 89, in _initialise raise ImportError(msg) This is preventing it from opening the GUI. Do you have any idea what should I do to avoid this. Thanks for your help. Rhitankar On Sat, May 4, 2013 at 6:21 AM, Thomas Holder wrote: Hi Rhitankar, looks like you installed the python3 version of Pmw which is not compatible with python 2.7. Cheers, Thomas Rhitankar Pal wrote, On 05/03/13 21:16: Dear Pymol developers, I have recently installed pymol 1.6.x in MAC OS X 10.8.2 and have the following error while opening the GUI Traceback (most recent call last): File /Library/Python/2.7/site-packages/pmg_tk/__init__.py, line 35, in run PMGApp(pymol_instance,skin).run(poll) File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 325, in __init__ self.runSkin() File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 251, in runSkin self.skin.setup() File /Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py, line 3661, in setup self.createInterface() File /Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py, line 3634, in createInterface self.balloon = Pmw.Balloon(self.root) File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBalloon.py, line 28, in __init__ Pmw.MegaToplevel.__init__(self, parent) File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBase.py, line 982, in __init__ super().__init__(parent, tkinter.Toplevel) TypeError: super() takes at least 1 argument (0 given) As a result it never opens the The Pymol Molecular Graphics System window. Can anyone help to find out what might be wrong. Thanks Rhitankar -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ 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 error
Hi Rhitankar, this depends which python you used and which arguments you passed to setup.py. I assume you used system python and no arguments, then just remove these: /Library/Python/2.7/site-packages/pymol /usr/local/bin/pymol Cheers, Thomas Rhitankar Pal wrote, On 05/08/13 18:46: Dear Thomas, Thanks for the informations. I think I am able to use port to install the pymol1.5 version but I would also need to remove the existing 1.6 version. Can you tell me the command to uninstall the existing version and then do a fresh installation? Thanks again Rhitankar On Wed, May 8, 2013 at 12:34 PM, Thomas Holder wrote: Dear Rhitankar, I should point out that Schrödinger also sells pre-compiled PyMOL with easy to use installers. http://pymol.org/academic.html Open-Source PyMOL was always targeted to power-users who are familiar with compiling software themselves. Regarding your question: It will most likely not be possible to compile and install open-source PyMOL with the system python on Mac, because OSX ships with an incompatible Tkinter library. So Pmw won't be your last problem. With macports it should work fine if you do this (see also David's answers): sudo port install tcl -corefoundation +threads sudo port install tk -quartz +x11 sudo port install pymol Hope that helps. Cheers, Thomas Rhitankar Pal wrote, On 05/08/13 18:01: Dear Thomas, Even after I installed the Pmw1.3 which should be compatible with python2.7 and reinstalling the pymol, I am still the following error message. File /Library/Python/2.7/site-packages/pymol/__init__.py, line 450, in launch_gui __import__(self.invocation.options.gui) File /Library/Python/2.7/site-packages/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 33, in module class PMGApp(Pmw.MegaWidget): File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py, line 131, in __getattr__ self._initialise() File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py, line 89, in _initialise raise ImportError(msg) This is preventing it from opening the GUI. Do you have any idea what should I do to avoid this. Thanks for your help. Rhitankar On Sat, May 4, 2013 at 6:21 AM, Thomas Holder wrote: Hi Rhitankar, looks like you installed the python3 version of Pmw which is not compatible with python 2.7. Cheers, Thomas Rhitankar Pal wrote, On 05/03/13 21:16: Dear Pymol developers, I have recently installed pymol 1.6.x in MAC OS X 10.8.2 and have the following error while opening the GUI Traceback (most recent call last): File /Library/Python/2.7/site-packages/pmg_tk/__init__.py, line 35, in run PMGApp(pymol_instance,skin).run(poll) File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 325, in __init__ self.runSkin() File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 251, in runSkin self.skin.setup() File /Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py, line 3661, in setup self.createInterface() File /Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py, line 3634, in createInterface self.balloon = Pmw.Balloon(self.root) File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBalloon.py, line 28, in __init__ Pmw.MegaToplevel.__init__(self, parent) File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBase.py, line 982, in __init__ super().__init__(parent, tkinter.Toplevel) TypeError: super() takes at least 1 argument (0 given) As a result it never opens the The Pymol Molecular Graphics System window. Can anyone help to find out what might be wrong. Thanks Rhitankar -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed
Re: [PyMOL] Secondary structure labeling
Hi Bishwa, what you want is to label one representative atom per secondary structure element. So figure out chain and residue number of those atoms, and label each of them individually: PyMOL label A/42/CA, beta1 PyMOL label A/117/CA, alpha1 PyMOL label A/147/CA, alpha2 For changing label font, size, color etc., see: http://pymolwiki.org/index.php/Label Cheers, Thomas Bishwa Subedi wrote, On 05/08/13 21:50: Dear Thomas, Thank you. The one you said is to show molecule as cartoon and color according to the secondary structure. But I would like to label/name the alpha helices as alpha1...and beta strands as Beta1 and so on. Can that be done using Pymol. Best Bishwa Subedi, M.Sc Bioinformatics University of Turku Finland On May 8, 2013, at 5:33 PM, Thomas Holder wrote: Hi Bishwa, can you be more precise what you mean by label? If the secondary structure is defined in the header of your PDB file, PyMOL can show cartoon representation, show text labels on C-alpha atoms and color by secondary structure. PyMOL as cartoon PyMOL label name CA, ss PyMOL color red, ss H PyMOL color yellow, ss S Cheers, Thomas Bishwa Subedi wrote, On 05/08/13 13:33: Hi All, I am using Pymol to make figures for my publication. I am not sure if there has been a discussion earlier but I would like to know how we can label the secondary structures (helices and strands) using Pymol. I have them defined in my header file using DSSP. Thank you in advance. Bishwa Subedi -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ 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 error
Hi Rhitankar, looks like you installed the python3 version of Pmw which is not compatible with python 2.7. Cheers, Thomas Rhitankar Pal wrote, On 05/03/13 21:16: Dear Pymol developers, I have recently installed pymol 1.6.x in MAC OS X 10.8.2 and have the following error while opening the GUI Traceback (most recent call last): File /Library/Python/2.7/site-packages/pmg_tk/__init__.py, line 35, in run PMGApp(pymol_instance,skin).run(poll) File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 325, in __init__ self.runSkin() File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 251, in runSkin self.skin.setup() File /Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py, line 3661, in setup self.createInterface() File /Library/Python/2.7/site-packages/pmg_tk/skins/normal/__init__.py, line 3634, in createInterface self.balloon = Pmw.Balloon(self.root) File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBalloon.py, line 28, in __init__ Pmw.MegaToplevel.__init__(self, parent) File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwBase.py, line 982, in __init__ super().__init__(parent, tkinter.Toplevel) TypeError: super() takes at least 1 argument (0 given) As a result it never opens the The Pymol Molecular Graphics System window. Can anyone help to find out what might be wrong. Thanks Rhitankar -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ 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] extra bonds
Hi Jianghai, by default PyMOL does a distance based bonding (basically when the VDW radii of two atoms overlap, they get connected). To prevent that, you need two settings: # before saving the correctly bonded but distorted structure set pdb_conect_all # before loading set connect_mode, 1 http://pymolwiki.org/index.php/connect_mode Cheers, Thomas Jianghai Zhu wrote, On 04/30/13 02:39: Hi, In my trajectory movie, there are some minor distortions of some of the residues, but the sticks presentation in pymol seems fine. However, after I loaded the trajectory pdb file use discrete=1, extra bonds would be shown in sticks in those slightly distorted residues. Is there is way to avoid those extra bonds? Thanks a lot. --Jianghai -- 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
Re: [PyMOL] Transparency of VASCo surfaces
Hi Gianluigi, that surface is a CGO object, so you need: set cgo_transparency, value, object Hope that helps. Cheers, Thomas Gianluigi Caltabiano wrote, On 04/22/13 18:49: Hi all, I often use VASCo surfaces and I am experiencing a strange behaviour on transparency settings as VASCo surfaces do not respond to: set transparency, value, object Not from the command line, not from the plugin itself. Pymol's surfaces get transparent but not the object corresponding to VASCo surface. I am not sure but I would say it worked to me before. I am on pymol 1.5.0.3 on a Macbook pro 2011 (Pymol Hybrid). Am I missing something? thanks and regards Gianluigi -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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] Fwd: Translate command seems to translate along an arbitrary axis
Hi Kyle, the translate command has a camera argument, which controls whether the vector is in camera space (default) or in model space. You want model space, so you need: PyMOLtranslate [1, 0, 0], glycan*, camera=0 Cheers, Thomas Kyle Sutherland-Cash wrote, On 04/17/13 19:47: Hello everyone, I've been trying to write a script to orient two particular molecules with respect to one another. I do this by calculating a translation vector between the two and then using cmd.translate to move the second object to the desired location. However, this didn't seem to have the desired effect and moved the second molecule somewhere else. I investigated further and tried using a translation of [1, 0, 0], which I supposed would just alter the x coordinate of my molecule. Instead it translated the molecule by 1A (I checked the magnitude of the actual translation to be sure) along an arbitrary axis. This axis also changed after deleting and recreating the object with its original coordinates. Am I doing something wrong, or did I not understand properly how translate works? I've pasted some sample input/output just below. Thanks, Kyle First time: PyMOLiterate_state 1, glycan* and id 1, print x, y, z 3.3945341 1.4326853 -0.0 IterateState: iterated over 1 atom coordinate states. PyMOLtranslate [1, 0, 0], glycan* PyMOLiterate_state 1, glycan* and id 1, print x, y, z 3.77618098259 2.14793467522 -0.585493266582 IterateState: iterated over 1 atom coordinate states. Second time: PyMOLiterate_state 1, glycan* and id 1, print x, y, z 3.3945341 1.4326853 -0.0 IterateState: iterated over 1 atom coordinate states. PyMOLtranslate [1, 0, 0], glycan* PyMOLiterate_state 1, glycan* and id 1, print x, y, z 2.96896576881 2.08610153198 -0.626740753651 IterateState: iterated over 1 atom coordinate states. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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
Re: [PyMOL] CGO fixed in space
Hi Steve, yes, the scene command has a message argument: PyMOL scene ? Usage: scene [ key [, action [, message [, view [, color [, active [, rep [, frame [, animate [, new_key [, hand [, quiet Example: PyMOL scene 001, store, Your Message Here Cheers, Thomas Soisson, Stephen M wrote, On 04/16/13 14:43: Is there a way to associate a wizard message with stored scenes so that the message changes with each scene? Thanks- Steve -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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
Re: [PyMOL] Reset Default Carbon Color
Hi Wilson, interesting question and actually there is no command to control this. Howevery, it's possible, there is a setting which doesn't have a name. In the latest 1.6alpha, you can do: # reset color cycle cmd.set(239, 0) In older PyMOL versions, this should work: # reset color cycle _cmd.set(cmd._COb, 239, (2, (0,)), '', -1, 1, 0) Some related notes: - auto and current are color names which correspond to the cycle - You can also disable the color cycling: set auto_color, off Cheers, Thomas Wilson Omesiete wrote, On 04/10/13 09:03: I noticed that the default carbon color for loaded objects is set to cycle from green to pink and then repeat to differentiate models. I have a lot of models being loading and deleted within one session, and it would be very useful to be able to reset that cycle, So that the first model after a reset will have green carbons, the second will have cyan carbons, and so on. This way my coloring patterns would be consistent. The reset function does not affect the cba* cycle, and I know that I could manually call the cba* variants after every file is loaded to force this functionality, but I would rather avoid that if possible. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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
Re: [PyMOL] conect records?
Hi Boris, can you be more precise with your question? What file type did you load (pdb?), which connections (I assume you mean bonds) are wrong? Cheers, Thomas Boris Kheyfets wrote, On 04/09/13 19:30: Hello PyMOL users, I study system which has 160919 residues, and 217021 atoms (it is initially a gromacs' gro file). Is there a way I can display conections correctly in PyMOL? -- With great respect, Boris. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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
Re: [PyMOL] export sequence alignment
Hi Joel, you can save alignment objects to clustalw format with the save command. Creating alignment objects with cealign is supported since version 1.5.0.5. The latest 1.6alpha also fixed swapped mobile/target arguments for creating alignment objects (only matters if aligning more than 2 structures). PyMOL fetch 1oky 1pkg 1t45, async=0 PyMOL remove not chain A PyMOL cealign 1oky, 1pkg, object=aln PyMOL cealign 1oky, 1t45, object=aln PyMOL save alignment.aln, aln Also keep in mind that this is a all-to-one alignment, not a real multiple (all-to-all) alignment. Cheers, Thomas Joel Tyndall wrote, On 04/08/13 01:05: Sorry forgot to add, I want to use multiple structures Hi folks, Sorry if this has already been asked but can I export the sequence alignment from PyMOL? I am looking to use cealign to do this (on windows) and I need the structural alignment based sequence alignment. Other tools maybe? I have mustang already Cheers Joel -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ 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] movie for morphing
Hi Jianghai, if your morph has 30 states, this short script will y-rock at the beginning, the middle, and the end or the morph: mset 1 x51 -15 x61 -30 x51 movie.rock 1, 40 movie.rock 76, 115 movie.rock 151, 190 Instead of movie.rock, you can also use movie.nutate of course. See also: http://pymolwiki.org/index.php/Mset Cheers, Thomas Jianghai Zhu wrote, On 04/05/13 20:59: Hi, I have a pdb containing the morphing. I can play the movie with the loaded pdb file. Now I want to start the movie with rocking the first state for a few seconds and end the movie with rocking the last state for a few seconds. How do I do that? Can I rock or nutate a state in the middle for a few seconds as well? Thanks. --Jianghai -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ 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 do you list H-bonds in pymol?
Hi Mina, Badoo Mina wrote, On 04/05/13 16:49: This is my first post to the group. I hope it would be a great experience :) I hope so too :) I am trying to compare the H-bonds in two NMR strcutures. So, I need to calculate H-bonds with a cutoff 2.5 and angle 35 angestrom that are availbale in 10 structures out of 20. I run list_hbonds.py as below: list_hb, selection1, cutoff=2.5, angle=35 but it doesn not meet what I want. Can you be more precise why it does not meet what you want? What result do you get, and what result do you expect? I would use the hb_list script like this: PyMOL fetch 2m1c, async=0 PyMOL split_states 2m1c, prefix=s PyMOL list_hb s_0001, cutoff=2.5, angle=35, hb_list_name=hb1 PyMOL list_hb s_0002, cutoff=2.5, angle=35, hb_list_name=hb2 PyMOL list_hb s_0003, cutoff=2.5, angle=35, hb_list_name=hb3 ... I want to look at inter and intra H-bonds (between two complexes of the protein and in each chain, too). How can I do that when I have splitted the ensemble to the 20 structures in pymol? Actually I would be prefer PyMOL's distance command for such a job, it works on all states at once, so you don't need to split states. PyMOL fetch 2m1c, async=0 PyMOL set h_bond_max_angle, 35 PyMOL distance hbAB, chain A, chain B, 2.5, mode=2 PyMOL distance hbAA, chain A, chain A, 2.5, mode=2 PyMOL distance hbBB, chain B, chain B, 2.5, mode=2 This doesn't print the H-bond pairs to the console output. If you need that, use this script: http://pymolwiki.org/index.php/Get_raw_distances See also: http://pymolwiki.org/index.php/Distance Hope that helps. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ 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 Testing Framework
Dear PyMOL users, We created a Python unittest framework for PyMOL. Our goals are to have complete test coverage of PyMOL's Python API and to have a regression test for each bug report. We made this openly accessible via Github. Now you can clone the repository, write some tests, and share them with the PyMOL community. So, please feel free to jump in and contribute! The code and basic directions can be found on Github: https://github.com/schrodinger/pymol-testing Happy testing! Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ 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] loadDir script
Hi James, please try, after loading the files: PyMOL order *, yes Cheers, Thomas James Starlight wrote, On 04/02/13 19:28: Pete, thanks for suggestion. I've tried to use loadDir with the pdb's subset where each file had name like 001.pdb 002.pdb ... 055.pdb but when the sotring have been still wrong :( also is loadDir script I found block for c in glob( g ): cmd.load(c) if ( group != None ): cmd.group( group, basename(c).split(.)[0], add ) what should I change here to sort files correctly? James -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html ___ 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 with h_add hydrogens in sequence viewer
Hi Matt, use the sort command after adding atoms: PyMOL h_add 1ycr PyMOL sort See also: http://pymolwiki.org/index.php/Sort Cheers, Thomas Matthew Baumgartner wrote, On 03/26/13 13:59: Hi, When I fetch a new structure (1YCR, for example) then run 'h_add 1ycr' the hydrogens are added to the structure as expected, but they are put in the sequence viewer as their own residue with the same chain. This is problematic for several reasons, one is that it breaks selections, when I click on a heavy atom of a residue (in residue selection mode) only the heavy atoms are selected and not the hydrogens. Also, if I save the structure to an pdb file, all of the hydrogens for the whole structure are placed at the beginning or the end of the structure, which makes them difficult to be interpreted by other programs (babel, chimera, namd, etc). I am using Pymol 1.5.0.1. (I will be updating to 1.6 soon). Any suggestions for settings to change or a workaround (possibly involving other programs, if necessary), would be greatly appreciated. Thanks, Matt -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ 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] Color changes during a morph
Hi Max, you use a named color newcolor and change it's values at each iteration, but all states refer to this same color. Before I show you how to fix your script, could you give spectrum_states from the PyMOLWiki a try? It's a script which does exactly what you want: http://pymolwiki.org/index.php/Spectrum_states PyMOL run spectrum_states.py PyMOL spectrum_states resi 430-572, surface sphere, green magenta Cheers, Thomas Max NANAO wrote, On 03/25/13 21:27: Hi All, Can anyone tell me how I might change the colors of a specific selection during the course of a rigimol generated morph? I would like one domain to go from purple to green, and have so far been unable to figure out how to do it. I tried coloring the different start/final states before rigimol-ing but that did not work. I have also tried to script the state coloring, as described here:http://www.pymolwiki.org/index.php/Color#Color_States_Individually. The problem is that cmd.set(surface_color, newcolor, resi 430:572, a) for example, where a is the state, does not seem to work at all. i.e. the color is not changed. The idea was to change the colors as follows: states = 30 for a in range(0,states): incr = 1.0/(states-1) r = 1.0-a*incr g = a*incr b = 1.0-a*incr col = [+str(r)+,+str(g)+,+str(b)+] cmd.set_color(newcolor,col) print COL state +str(a+1)+: +col cmd.set(surface_color, newcolor, resi 430:572, a) cmd.set(sphere_color,newcolor, resi 430:572, a) cmd.recolor() ugly, I know! this is 64 bit pymol 1.5.0.6 eval for linux. Thanks in advance, Max -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ 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 1.6 pre-release announcement
Hi Christoph,
thanks a lot for the patches.
Regarding your suggestion for pymol.bat: I guess this will not work if
you install with a custom prefix, since you make assumptions where to
find pythonw.exe and the pymol module.
I suggest to discuss this off-list, since it's quite specific.
Cheers,
Thomas
Christoph Gohlke wrote, On 03/25/13 18:11:
On 3/24/2013 3:02 AM, Thomas Holder wrote:
Dear PyMOL users,
The pre-release version of PyMOL 1.6 has been pushed to the open
source repository on SourceForge. Besides several minor fixes and
improvements, this version should complete the transition to
shader-based rendering for all on-screen drawing. For non-integrated
chipsets this typically means higher quality and quicker rendering.
Please also note that the URL of the SVN repository changed due to an
upgrade of the SourceForge website:
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
As always, we welcome bug reports and positive feedback.
Cheers,
- The PyMOL Team at Schrödinger
Hello,
Please consider the attached changes for building with msvc on Windows.
Also, the latest changes to vmdir.h don't compile with msvc.
http://sourceforge.net/p/pymol/code/4025/tree//trunk/pymol/contrib/uiuc/plugins/molfile_plugin/src/vmddir.h?diff=50c0fc56e88f3d0bdf694277:4024
Opening absolute paths does not work on Windows (e.g. C:\1bna.pdb):
Index: pymol/modules/pymol/internal.py
===
--- pymol/modules/pymol/internal.py(revision 4025)
+++ pymol/modules/pymol/internal.py(working copy)
@@ -303,7 +303,7 @@
try:
if not isinstance(finfo, basestring):
handle = finfo
-elif ':' in finfo:
+elif '://' in finfo:
import urllib
handle = urllib.urlopen(finfo)
else:
The launch script, Scripts\pymol.bat, seems overly complicated and
doesn't always work for binary installers. Suggestion:
Index: pymol/setup.py
===
--- pymol/setup.py(revision 4025)
+++ pymol/setup.py(working copy)
@@ -119,9 +119,7 @@
with open(launch_script, 'w') as out:
if sys.platform.startswith('win'):
-out.write('set PYMOL_PATH=' + pymol_path + os.linesep)
-out.write('%s %s' % (python_exe, pymol_file))
-out.write(' %1 %2 %3 %4 %5 %6 %7 %8 %9' + os.linesep)
+out.write(r'@%~dp0\..\pythonw.exe -m pymol.__init__ %*')
else:
out.write('#!/bin/sh' + os.linesep)
if sys.platform.startswith('darwin'):
Thanks,
Christoph
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
--
Own the Future-Intelreg; Level Up Game Demo Contest 2013
Rise to greatness in Intel's independent game demo contest.
Compete for recognition, cash, and the chance to get your game
on Steam. $5K grand prize plus 10 genre and skill prizes.
Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d
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[PyMOL] PyMOL 1.6 pre-release announcement
Dear PyMOL users, The pre-release version of PyMOL 1.6 has been pushed to the open source repository on SourceForge. Besides several minor fixes and improvements, this version should complete the transition to shader-based rendering for all on-screen drawing. For non-integrated chipsets this typically means higher quality and quicker rendering. Please also note that the URL of the SVN repository changed due to an upgrade of the SourceForge website: svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol As always, we welcome bug reports and positive feedback. Cheers, - The PyMOL Team at Schrödinger -- 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_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
Re: [PyMOL] PyMOL 1.6 pre-release announcement
Hi Michael, I haven't tagged that commit. It's svn revision 4025. For the final 1.6.0 version we will upload a tar.gz archive to sourceforge. Cheers, Thomas On Mar 24, 2013, at 1:18 PM, Michael Banck mba...@debian.org wrote: Hi, On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote: The pre-release version of PyMOL 1.6 has been pushed to the open source repository on SourceForge. Besides several minor fixes and improvements, this version should complete the transition to shader-based rendering for all on-screen drawing. For non-integrated chipsets this typically means higher quality and quicker rendering. Please also note that the URL of the SVN repository changed due to an upgrade of the SourceForge website: svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol As always, we welcome bug reports and positive feedback. Great! Is there some pre-release version number assigned to that commit, like 1.6.0pre1 or 1.6.0rc1, assuming a final 1.6.0 will follow at some point? Best regards, Michael -- 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_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
Re: [PyMOL] Mesh Cavity Mode?
Hi Jared, how about: PyMOL as surface PyMOL set surface_cavity_mode, 1 PyMOL set surface_type, 2 Cheers, Thomas Sampson, Jared wrote, On 03/22/13 23:31: Hi all - Is there a way to show internal cavities as meshes instead of surfaces? Something like `set surface_cavity_mode, 1` except with mesh? Thanks in advance for responses. Cheers, Jared -- 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_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
Re: [PyMOL] (no subject)
Hi Nina Marie, I haven't tested that thoroughly, but for me Incentive PyMOL 1.5.0.5 runs fine on Windows 8. Cheers, Thomas Wolf, Nina Marie wrote, On 03/19/13 21:11: Hi, I recently upgraded my computer to windows 8. Since then, pymol will not open. Is the latest version of pymol incompatible with windows 8? Or is there something I can do to get it working on my computer? -- 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_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
Re: [PyMOL] Error while running a python script
Hi Bharat, you should run python scripts from within PyMOL using the run command: http://pymolwiki.org/index.php/Running_Scripts Or follow these examples if you really need to launch PyMOL from a python session (not recommended for beginners): http://pymolwiki.org/index.php/Launching_From_a_Script Cheers, Thomas bharat gupta wrote, On 03/20/13 03:23: Hi, I am a newbie in python scripting from pymol. I am getting the following error while using the command cmd.load :- from pymol import cmd print Current PyMoL Directory:, cmd.pwd() cmd.load (1A73.pdb) Error:- -- Traceback (most recent call last): File test.py, line 5, in module cmd.load (1A73.pdb) File /usr/lib/python2.7/site-packages/pymol/importing.py, line 872, in load _self.unlock(r,_self) File /usr/lib/python2.7/site-packages/pymol/locking.py, line 79, in unlock if (thread.get_ident() == pymol.glutThread): AttributeError: 'module' object has no attribute 'glutThread' Bharat -- 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_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
Re: [PyMOL] [Pymol] plugins won't intitialize
Hi Yarrow, I assume you don't have the latest PyMOL version (1.5), which has improved plugin support and should not raise such an error. I don't know movs.py but it looks like it has not been written as a plugin, but just a normal PyMOL/python script (again, PyMOL 1.5 will not make such a strong differentiation). Try to load the script with the run command on the command line: PyMOL run movs.py http://pymolwiki.org/index.php/Running_Scripts Hope that helps. Cheers, Thomas Yarrow Madrona wrote, On 03/16/13 02:10: 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 -- 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_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
Re: [PyMOL] How to ray trace clipped image without clipping spheres.
Along those lines: The script SelectClipped from the PyMOLWiki does a good job here, at least for spheres. http://pymolwiki.org/index.php/SelectClipped Example (after having loaded the script or installed it with the plugin manager): PyMOL select_clipped PyMOL hide everything, not clipped PyMOL clip atoms, 2, clipped Cheers, Thomas On Mar 11, 2013, at 4:38 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: # Hey :) # Here is a work around... # First import the numpy module import numpy # Then store the viewing matrix as 6 by 3 numpy array. M=numpy.array(cmd.get_view()).reshape(6,3) # Now place a pseudoatom at the position of the camera # Turn off autozoom to keep the view set auto_zoom, 0 scale=1.0 cmd.pseudoatom(dummy,pos=list(M[4,:]-scale*numpy.dot(M[:3,:3],M[3,:]))) # The dummy can now be used to hide all spheres within a cutoff distance. E.g. hide spheres, all within 150 of dummy # You may need to play with the distance to get the right effect. # It is possible to use the distances of the original clipping planes, # by extracting those from the viewing matrix. # The 'scale' parameter can be used to adjust the effect. # If scale 1, the dummy is placed behind the camera, which may be # required for a proper planar cut. # On the other hand, you can set it to 1, to put the dummy closer to # the scene and cut out a spherical region. # Note that you can change the view after this operation and have a nice sideview # of a clipped system, or use it to clip a system multiple times from different sides. # Enjoy! # Cheers, # Tsjerk -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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] refinement in morph
Hi Jianghai, you need to fix the jumping atoms before doing the refinement. Lets say you want to fix all chloride ions, it would look like this: # morph without refinement rigimol.morph(rin, rout, refinement=0, async=0) # get rid of the default movie cmd.mstop() cmd.frame(1) cmd.mset() # fix chlorides and run refinement cmd.flag(fix, elem CL) rigimol.refine(5, rout) Hope that helps. Cheers, Thomas On Mar 7, 2013, at 8:28 AM, Jianghai Zhu j...@idi.harvard.edu wrote: Hi, If I turn on the refinement option in morph, the non-covalently bonded atoms like metals and waters are moving around a lot. However, if I turn off the refinement, there are some distortions in my protein. Is there a way to make the non-covalently bonded atoms just move along the transition path? Thanks. --Jianghai -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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] running pse file in batch mode
Hi Jon, there is no need to convert the pse file into a script, just write a short script which loads the pse file in the beginning. load session.pse scene 001, recall viewport 800, 600 png scene001.png, ray=1 You can run that in batch mode. Cheers, Thomas On Mar 6, 2013, at 4:11 PM, Jonathan Grimes jonat...@strubi.ox.ac.uk wrote: I've have a pse file with a number of scenes defined. i would like to run the pse file without the gui…..but then select scenes via the external gui window….and render…… can i do this akin to batch mode ??? or can i convert the pse file into a pmol script ?? each scene will take 30mins to render i would also like to write out the scene as a vrml file…...i gave up after an hour at the graphics machine. many thanks for your help jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- 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
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
Re: [PyMOL] symmetry operation to generate the whole virus particle
Hi Yeping and Troels, symexp is unlikely to give you the REMARK 350 biomolecule, it is for generating neighboring symmetry mates of the crystallographic packing. The following scripts from the PyMOLWiki can read REMARK 350 and generate the biological unit: http://pymolwiki.org/index.php/Psico - biomolecule command http://pymolwiki.org/index.php/BiologicalUnit/Quat http://pymolwiki.org/index.php/BiologicalUnit Remember that you can also fetch the biomolecule as type=pdb1 for most structures. Example: fetch 2cas, type=pdb1, async=0 as ribbon set all_states Hope that helps. Cheers, Thomas Troels Emtekær Linnet wrote, On 02/28/13 11:38: You are probably looking for this: http://pymolwiki.org/index.php/Symexp Or else you can do it in CCP4. Coordinate utilities - Edit PDB file -Use pdbset - generate chains via symmetry operations Troels Emtekær Linnet Ved kløvermarken 9, 1.th http://1.th 2300 København S Mobil: +45 60210234 2013/2/28 yp sun sunyep...@yahoo.com.cn mailto:sunyep...@yahoo.com.cn Dear pymol users: Usually pymol can show only one chain when you open a pdb file of virus particles (such as 2buk,1sva, etc.). I am trying to create the whole virus particle and I know it may need applying symmetry operations. And these symmetry operation has been given in the pdb files. For example, the follow is the symmetry operation of 2buk: REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 But I don't understand how to do symmetry operations. Can pymol do these or other software is needed? Please help. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -- 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
Re: [PyMOL] Increase sphere size for heavy element
Hi Martin, PyMOL alter elem W, vdw=2.0 PyMOL rebuild Cheers, Thomas Martin Hediger wrote, On 02/26/13 08:38: Hi PyMOL users If I display these coordinates HETATM 38 C LIG 2 1.535 2.288 -4.156 1.00 0.00 C HETATM 39 C LIG 2 2.284 1.535 -3.066 1.00 0.00 C HETATM 40 O LIG 2 3.406 2.362 -2.714 1.00 0.00 O HETATM 41 C LIG 2 1.426 1.234 -1.850 1.00 0.00 C HETATM 42 S LIG 2 -0.260 0.689 -2.100 1.00 0.00 S HETATM 43 C LIG 2 1.886 1.450 -0.593 1.00 0.00 C HETATM 44 S LIG 2 0.838 1.262 0.813 1.00 0.00 S HETATM 45 C LIG 2 3.318 1.872 -0.336 1.00 0.00 C HETATM 46 C LIG 2 4.139 1.803 -1.624 1.00 0.00 C HETATM 47 W LIG 2 -1.132 -0.004 0.041 1.00 0.00 W HETATM 48 O LIG 2 0.155 -1.665 0.118 1.00 0.00 O HETATM 49 C LIG 2 0.721 -3.870 -0.567 1.00 0.00 C HETATM 50 C LIG 2 0.384 -2.594 -0.826 1.00 0.00 C HETATM 51 C LIG 2 -5.606 -3.611 -1.000 1.00 0.00 C HETATM 52 O LIG 2 -6.664 -4.080 -0.564 1.00 0.00 O HETATM 53 N LIG 2 -4.607 -4.417 -1.426 1.00 0.00 N using Preset/Ball-and-stick, the tungsten atom is drawn with a very small radius. Can this radius be increased? Thanks Martin -- 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
Re: [PyMOL] Display style for partial bond
Hi Martin, only distance measures can draw dashed lines in PyMOL, so try this: unbond elem W, elem C show sticks show sphere, elem W distance transbonds, elem W, elem C hide label set dash_round_ends, off set dash_radius, 0.2 set dash_length, 0.4 set dash_gap, 0.15 ray The dashes will display as nice cylinders when ray traced and also with the new shader rendering in PyMOL 1.5 (set use_shaders). Cheers, Thomas Martin Hediger wrote, On 02/26/13 09:57: Dear PyMOL Users If you load these coordinates in PyMOL HETATM1 W LIG 1 -1.357 -0.079 0.052 1.00 0.00 W HETATM2 C LIG 1 -0.713 -1.686 1.008 1.00 0.00 C HETATM3 C LIG 1 -0.323 -1.855 -0.270 1.00 0.00 C HETATM4 H LIG 1 -0.664 -2.180 1.970 1.00 0.00 H HETATM5 H LIG 1 -0.441 -2.597 -1.043 1.00 0.00 H you'll see that a bond between W and C is drawn. However, this is supposed to be a transition state, so a dashed bond would be more appropriate. Can this somehow be drawn? Thanks, Martin -- 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
Re: [PyMOL] About draw_links.py by Dr. Robert Campbell
in the most recent version of PyMOL, which can render measurement objects with shaders, you can also use the distance command to get a similar result: set use_shaders set dash_gap, 0 distance sele and n. CA, sele and n. CA Cheers, Thomas On Feb 21, 2013, at 10:11 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi, If you want to draw all bonds for all pairs between two selections, you can just use bond: bond sele and n. ca, sele and n. ca Hope it helps, Tsjerk On Thu, Feb 21, 2013 at 9:19 PM, Robert Campbell robert.campb...@queensu.ca wrote: Hi Anasuya, On Thu, 21 Feb 2013 17:10:40 +0530 Anasuya Dighe anas...@mbu.iisc.ernet.in wrote: Hi, I have been trying to use the script draw_links.py at http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ to view links between each pair of c-alpha atoms present in an atom selection. Once I load a PDB (1q16.pdb) and make an atom selection, lets say : PyMOLselect pk1, name CA in resi 5+10+15+12+16 and chain C , on the PyMOLcommand-line in pymol, I do : PyMOLrun draw_links.py I wanted to visualise links between all pairs of calpha atoms present in the atom selection, pk1. However I am unable to do that using draw_links.py I am doing: PyMOL draw_links pk1 How can I do this using draw_links.py? Where am I going wrong? Perhaps the instructions are not clear enough, but the script is not designed to automatically draw links between all pairs of C-alphas in a selection. It expects two different selections and it will draw links between the first residue of each selection and then the second and so on. It doesn't therefore make sense to give it the same selection for both because, in your example, it draws a zero-length link between residue 5 and residue 5, and another between residue 10 and residue 10 and so on. You will have to run the script multiple times to get the links you want: draw_links name CA resi 5 and chain C, name CA resi 10 and chain C draw_links name CA resi 5 and chain C, name CA resi 15 and chain C draw_links name CA resi 5 and chain C, name CA resi 12 and chain C Sorry that it doesn't quite do what you were expecting! I designed it for the situation where I have two structures that exhibit a conformational change and I wanted to show how the C-alphas were moving so then it made sense to have the two selections be the same atoms, but in different molecules. Cheers, Rob -- 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
Re: [PyMOL] constant distances over states
Hi Jordan, distance measurements actually should be multistate by default. Do you create those with a script and provide the state argument? # create multi-state measurement (default) distance test, pk1, pk2, state=0 # create only for state 1 distance test, pk1, pk2, state=1 Cheers, Thomas Jordan Willis wrote, On 02/21/13 06:46: Hi everyone, I was wondering if there is an easy way to show distances as a function of state. As you show each state (using the play button or mplay), can you show the distance measurement changing? For now it just keeps the distance of the first state shown. I could script this but first would like to ask the users group if there is an easier alternative. Jordan -- 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
Re: [PyMOL] VMD module in Rev 4019-4020 break build
Hi Quyen, sorry for that, I added the missing file in rev 4020. Cheers, Thomas QT wrote, On 02/16/13 00:58: Dear pymol users, Revision 4019 added a bunch of changes to the VMD module and three files require gmplugin.h that is missing from the module src directory moldenplugin.c:38:#include qmplugin.h basissetplugin.c:43:#include qmplugin.h gamessplugin.c:160:#include qmplugin.h Please fix =) Best, Quyen -- Thomas Holder PyMOL Developer Schrödinger Contractor -- The Go Parallel Website, sponsored by Intel - in partnership with Geeknet, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials, tech docs, whitepapers, evaluation guides, and opinion stories. Check out the most recent posts - 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] setup.py and VMD plugins updated
Greetings, this is a quick announcement about the latest commits to SVN regarding the build system. - setup2.py is no longer needed, this is all done by setup.py now - experimental support for parallel and incremental build - VMD plugins enabled by default - new install options --pymol-path and --bundled-pmw Please report any bugs or problems that you encounter. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- The Go Parallel Website, sponsored by Intel - in partnership with Geeknet, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials, tech docs, whitepapers, evaluation guides, and opinion stories. Check out the most recent posts - 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] Path problem when running a script
Hi Jens, the run command is not identical to the python import statement. It does not search sys.path but takes an absolute or relative (from the current working directory) file name. Both of these will work: PyMOLrun /opt/pymol/scripts/align_all.py PyMOLimport align_all See also: http://pymolwiki.org/index.php/Run http://pymolwiki.org/index.php/Pwd Cheers, Thomas Thomas, Jens wrote, On 02/12/13 10:47: Hi, I'm trying to run the align_all.py script (http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/align_all.py) in PyMol running on Linux. I've put the script in /opt/pymol/scripts, and in my .pymolrc file, I have the following: sys.path.append(/opt/pymol/scripts) and if I print sys.path in the pymol command line, I get the following: PyMOLprint sys.path ['', '/opt/pymol/modules', '/opt/pymol/ext/lib/python2.5/site-packages/setuptools-0.6c7-py2.5.egg', '/opt/pymol/ext/lib/python2.5/site-packages/simplejson-2.0.5-py2.5-linux-i686.egg', '/opt/pymol/ext/lib/python25.zip', '/opt/pymol/ext/lib/python2.5', '/opt/pymol/ext/lib/python2.5/plat-linux2', '/opt/pymol/ext/lib/python2.5/lib-tk', '/opt/pymol/ext/lib/python2.5/lib-dynload', '/opt/pymol/ext/lib/python2.5/site-packages', '/opt/pymol/scripts'] However, if I try running the script, I get the following: PyMOLrun align_all.py Traceback (most recent call last): File /home/vertrees/work/products/pymol/edu_build/dist/pymol/./modules/pymol/parser.py, line 338, in parse File /opt/pymol/modules/pymol/parsing.py, line 455, in run_file execfile(file,global_ns,local_ns) IOError: [Errno 2] No such file or directory: 'align_all.py' If I run the full path to the script it works: PyMOLrun /opt/pymol/scripts/align_all.py And I can then use the command. Is there any obvious reason why it's not looking in the /opt/pymol/scripts directory, even when this is in the sys.path? Thanks, Jens -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-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
Re: [PyMOL] problem setting up morph under eMovie
Hi Michael, have you tried to use the command line for morphing? Have a look at the example section of http://pymolwiki.org/index.php/Morph Regarding the eMovie button, I'll forward the question to the eMovie author, he should know the answer. Cheers, Thomas Michael L Oldham wrote, On 02/04/13 15:18: My institution a subscription to incentive PyMol. In the past, I have used the morph that appeared under the list of eMovie commands but now it does not appear. I am not sure what i am missing: a vaild rigimol file, the wrong version (currently using Version 1.5.0.4). Regardless I also need instructions for how to embed the morph in the list of commands. Any help would be greatly appreciated. Thanks -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-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
Re: [PyMOL] rainbow coloring from the N to C terminus of multiple backbones shown as ribbons
Hi Ali, paste this into the PyMOL command line: unset ribbon_color, (*) set ribbon_color, default for name in cmd.get_object_list(): \ cmd.spectrum(selection=name + and polymer) This will do rainbow coloring on each object separately. The ribbon_color setting will override atom colors, that's the reason why selecting color/rainbow from the menu has no effect in your session. Hope that helps. Cheers, Thomas Muhammad Naqvi wrote, On 02/04/13 18:38: Hi Folks, I have about 2000 pdb files loaded into one session, with their backbones shown as ribbons, that have been aligned by select residues ranging from 15-19 using the align_all command. The problem I have is coloring, right now I have to manually color in rainbow into all of the residues by using the command: set ribbon_color, color name, resi __#__ but the transitions are not smooth. In addition, selecting color/rainbow using the all entry does not do anything to the color. Changing the color manually for each entry, however, works well. I can manually select the color button on each of the pdb entries and select rainbow, but its not feasible to do for 2000 entries. I was wondering if there is an automated way of coloring each ribbon end to end in the same rainbow. Best Regards, Ali -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-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
Re: [PyMOL] default settings
Hi Adam and Nat, a few clarifying remarks on this topic: - The leading dot is optional, so everything that starts with .pymolrc or pymolrc will be found by PyMOL. Files with dot take precedence over files without dot. - Files ending on .py (or .pym) will be parsed as python scripts, files ending on .pml (or .p1m) or without suffix will be parsed as PyMOL command syntax. - Several directories are searched, in order: - $HOME - $HOMEPATH + $HOMEDRIVE (on Windows) - $PYMOL_PATH - PyMOL will even load multiple pymolrc files, however only either with dot or without dot, and only from the same directory. I'll update the PyMOLWiki with that information. A handy script for saving the current set of changed settings to a pymolrc file is available here: http://pymolwiki.org/index.php/Save_settings Cheers, Thomas H. Adam Steinberg wrote, On 01/30/13 20:37: 1st, thank you for your patience and help. 2nd, for those who end up trying to also do this… Apple now hides all files in the user folder that start with a period. Therefore, the minute you hit enter after changing the name to .pymolrc, the file disappears. You have to run a third party app that allows you to see the hidden files. I used TinkerTool. This works and solved the problem! Thanks! On Jan 30, 2013, at 12:59 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Wed, Jan 30, 2013 at 10:56 AM, H. Adam Steinberg a...@steinbergs.us wrote: You are correct, if I put the pymolrc.pym file in the user folder, MacPyMol does try to read it when it starts up. However, it errors every time. If I put just this one command in the file and start up PyMol, it comes back with: File /Users/adam/pymolrc.pym, line 1 set auto_zoom = 0 ^ SyntaxError: invalid syntax That's because you're using the wrong file name: On a linux-type system, this file will be located in /path/to/home/.pymolrc. -Nat -- 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_jan ___ 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] Hight-quality visualisation
Hi James, to decrease the width of the contour line, render the image with a larger size and then eventually scale it down again with some image manipulation tool (photoshop, imagemagick, ...). ray 1600, 1200 Cheers, Thomas On Jan 26, 2013, at 8:03 AM, James Starlight jmsstarli...@gmail.com wrote: Dear PyMol users! I wounder to know about all possible options of high-quality image's visualisation by means of Ray command. Below you can see list of commands which I've already tried set ray_trace_mode, 3; #set ray_trace_fog,0 #set ray_shadows,0 set antialias, 2 ray 800, 600 In particular I wounder to know how I could decrease width of contour black line (appeared in set ray_trace_mode) ? Also I'd like to show more examples besides those which I found here http://www.pymolwiki.org/index.php/Ray_trace_mode#Modes James -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ 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] Saving setting in PyMol
Hi James, PyMOL itself does not install a .pymolrc file, but you can create your own and put it in your home directory. On startup, PyMOL will search a couple of places for the .pymolrc file (current directory, home directory, PYMOL_PATH) and take the first that is found. Hope that helps. Cheers, Thomas On Jan 26, 2013, at 7:14 AM, James Starlight jmsstarli...@gmail.com wrote: Recently I've tried to find pymolrc but couldn't do it ( I have pymol 1.5 installed from binarries package manager ) own@starlight ~/Desktop $ locate pymolrc own@starlight ~/Desktop $ locate .pymolrc own@starlight ~/Desktop $ locate *.pymolrc How I could locate it ? Akso I'm looking for detailed options of the possible settings in that file ( e.g I didnt find how to set maximum quality of images as the default option ) Thanks for help James -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ 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] echo colour
Hi Joel, the color is stored as a numeric atom property, you can use iterate to get it. PyMOL iterate (first objX), print color If you need the name of the color, get the index to name mapping as a dictionary from PyMOL like this: PyMOL stored.cn = dict((i,c) for (c,i) in cmd.get_color_indices()) PyMOL iterate (first objX), print stored.cn[color] Last but not least, there is the psico.querying.get_color function in the PSICO module :) Cheers, Thomas Joel Tyndall wrote, On 01/23/13 02:04: Hi list, With the myriad of colours in Pymol, I tend to forget which shade of what I have used. Is there a way/command to print the colour I have used to colour object X? Cheers Joel _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d ___ 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 do I get current selection name from python?
http://docs.python.org/2/library/tempfile.html#tempfile.NamedTemporaryFile
Quote: If delete is true (the default), the file is deleted as soon as
it is closed.
Cheers,
Thomas
Boris Kheyfets wrote, On 01/23/13 14:47:
It prints the selection all right. Why then save wouldn't save it:
def bk_saves_unique_pdb(Selection = None):
Takes current selection (or all -- if nothing selected) and saves it
as a uniquetly named pdb file (Frame_Selection_RandomString.pdb) in the
current working directory.
if not Selection:
Selection = cmd.get_names('selections', 1)
if Selection:
Selection = Selection[0] # it was a list
else:
Selection = 'all'
tempFile = tempfile.NamedTemporaryFile(dir=os.curdir,
prefix={frame:03d}_{sel}_.format(frame=cmd.get_frame(), sel=Selection) ,
suffix=.pdb)
print tempFile.name, Selection # prints righteous file name and selection
name (though not in quotes)
cmd.save(tempFile.name, Selection) # but still saves nothing
cmd.extend(bk_saves_unique_pdb, bk_saves_unique_pdb)
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
--
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Re: [PyMOL] Renumber Script problem
Hi Alex, the renumber script only sets the residue number, it does not reorder atoms internally. Just type PyMOL sort to sort internally based on the new residue numbers. See also: http://pymolwiki.org/index.php/Sort Cheers, Thomas Alex Truong wrote, On 01/21/13 19:21: Hi All, I've been having a bit of trouble recently with the renumber script. I have a pdb file that I'm trying to renumber, but unlike the other times I've used it, it is renumbering incorrectly. The numbers are usually spaced out 5 residues apart, but I have one number right near the beginning that is 6 residues down from the previous one. Needless to say, this is screwing up the rest of the count. Is there any idea why? I've provided a screenshot. Thanks, Alex -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122412 ___ 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] Renumber Script problem
Hi Jordan,
nice script, but it does not do the same like the renumber script from
the PyMOLWiki (http://pymolwiki.org/index.php/Renumber). Try this: set
all residue numbers to 1, the renumber script will not care because it
walks along the bonds and increases the count whenever it passes a
peptide bond. The Biopython parser however will read just one residue.
Cheers,
Thomas
Jordan Willis wrote, On 01/21/13 19:53:
Does it have to be a pymol script. Renumbering pdbs is the bread and butter
of biopython pdb module:
#!/blue/meilerlab/apps/Linux2/x86_64/bin/python2.5
import sys
from Bio.PDB import *
from optparse import OptionParser
import warnings
def main():
usage = %prog input.pdb output.pdb
parser= OptionParser(usage)
parser.add_option(-n,dest=start,help=residue number to start with,
default is 1,default=1)
parser.add_option(--preserve,dest=preserve,help=preserve insertion
code and heteroflags,default=False, action=store_true)
parser.add_option(--norestart,dest=norestart,help=don't start
renumbering at each chain, default=False,default=False, action=store_true)
(options, args) = parser.parse_args()
warnings.simplefilter('ignore',PDBExceptions.PDBConstructionWarning)
PDBparse = PDBParser(PERMISSIVE=1)
struct = PDBparse.get_structure(args[0][0:3],args[0])
residue_id = int(options.start)
chain_id =
for residue in struct.get_residues():
chain = residue.get_parent()
if(chain_id != chain.get_id() and not options.norestart):
chain_id = chain.get_id()
residue_id=int(options.start)
if(options.preserve):
hetero = residue.id[0]
insert = residue.id[2]
residue.id=(hetero,residue_id,insert)
else:
residue.id=(' ',residue_id,' ')
residue_id +=1
io=PDBIO()
io.set_structure(struct)
io.save(args[1])
if __name__ == __main__:
main()
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Re: [PyMOL] DNA ligand presentation in PyMOL
Hi Amna, DNA molecule has internal HBONDS too.. how can i see the hbonds made between just ligand and DNA, ??? If there is nothing else than DNA and ligand, this should probably work (otherwise, be more precise with the selections...): PyMOL distance hbonds, (polymer), (organic), mode=2 how can i show just interacting residues of DNA with ligand i am unable to create this presentation.. PyMOL show sticks, (polymer) within 5 of (organic) Again, if polymer and organic are ambiguous, replace them with more explicit selections like (chain A and resi 34). http://pymolwiki.org/index.php/Single-word_Selectors http://pymolwiki.org/index.php/Selection_Algebra http://pymolwiki.org/index.php/Property_Selectors Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ 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] get_dihedral for multiple files(states of a movie)
Hi Tasneem, python for state in range(1, cmd.count_states() + 1): angle = cmd.get_dihedral(58/N, 58/C, 58/CA, 58/CB, state) print state, angle python end Cheers, Thomas Tasneem Ali wrote, On 01/10/13 17:08: Hello all, I have generated a movie of 300 snapshots (MD simulation trajectory). How can i calculate dihedral angles for same four atoms across the trajectory (or a movie)?? I mean get_dihedral 58/n,58/c,58/ca,58/cb values 300 times for each snapshot. Regards Tasneem -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ 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] DNA measurement help require by sculptor
Hi Briony, this sounds like a very cool project! Regarding question 1: If your PDB DNA model is long enough, you can use cafit_orientation from the psico module (a PyMOL extension) to draw the axis. It determines the axis by least-square linear fit on the backbone atoms. This requires a recent PyMOL version and numpy. If the helix is not long enough, cafit_orientation will most likely result in a slightly skewed axis, but I think you need a perfect axis, right? If you are interested, I could customize the script to take the bases orientations into account when interpolating the axis. Just let me know. http://www.pymolwiki.org/index.php/psico Cheers, Thomas Briony Marshall (Personal) wrote, On 01/07/13 17:43: Apologies - Slightly off topic request for collaboration from a sculptor, but it does relate to how Pymol works Dear all, I am a sculptor working on an ambitious bronze sculpture of DNA and I am looking to find out some more detailed measurements of ideal B-DNA which I am having difficulty getting from Pymol. You can see my previous work on my website: http://www.briony.com The sculpture I am making represents a single turn of ideal B-DNA at a scale of 500 million times life size, i.e. it will be 1m wide by 1.66m tall. Each atom is represented by a small human figure made of bronze, with the bonds between them represented by the arms and legs of the figures. (this is a much more complicated version of this sculpture I did previously based on the structure of diamond: http://www.briony.com/works/dream-II_1.html) I studied biochemistry at Oxford in the mid-90s and did a specialisation in DNA dynamics so I am not altogether wet behind the ears, but as I spend most of my time now with plaster and clay, my in depth DNA knowledge is a bit weak and I'm new to Pymol. I have been working from the ideal B-DNA PDB file for all my measurements. I am at the stage that I have made all 20 bases, and 20 sections of sugar phosphate backbone in bronze, and I am about to start constructing my double helix around a stainless steel central access. 1. I haven't worked out how to get the central axis of B-DNA to appear on Pymol. Is there a way to do this? If not, I would need a scale drawings of both base pairs with the central axis point (of B-DNA) marked. This would allow me to make various measurements to ensure I put the bases and sugar phospate sections together accurately. (In particular I need to know the distance between the central axis and the N of each base pair that attaches to the backbone, and the angle between these two lines within each base pair 'rung') 2. I was looking for advice on whether I can safely ignore the base pair axis inclination (as this is only 1.2° I think so) and the propelor twist of the base pairs (I was less sure about this). I think I can straightening up the base pairs but ensure that where they attach to the backbone stays in the same place. I'm hoping the only effect might be on the length and orientation of the hydrogen bonds. 3. Final question for now - is there a standard colour convention for representation of bases like there is for atoms? FYI, I had contemplated doing the patina (colouring) of the sculpture according to the atomic colour code, but with about 1000 atoms, this would be a very fiddly long job. I am now considering colouring each base a different colour and was wondering if there was a standard, such as Adenine is always represented blue, etc.. Many thanks in advance for any help you can give. Regards Briony Briony Marshall - Sculptor www.briony.com http://www.briony.com/ http://www.briony.com/join my mailing list: www.briony.com/subscribe.html http://www.briony.com/subscribe.html or like me on facebook: www.facebook.com/brionymarshallsculptor http://www.facebook.com/brionymarshallsculptor UK mobile: +44 (0)7956 107 893 Pangolin London Sculptor in Residence blog: www.a-n.co.uk/link/creative-year http://www.a-n.co.uk/link/creative-year -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ 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 visualization problem
Hi Abida, thanks for the PDB file that you sent me off-list. It is a naming conflict, you have more than one chain A which have overlapping residue numbers and even IDs. You can still load them like this: PyMOL set retain_order PyMOL load complex.1.pdb PyMOL as cartoon I also suggest to fix the chain identifier: PyMOL alter complex.1 and rank 3578-, chain=B PyMOL util.cbc And for the second file: PyMOL set retain_order PyMOL load complex.5.pdb PyMOL as cartoon PyMOL alter complex.5 and chain A and rank 1322-, chain=C PyMOL util.cbc Hope that helps. Cheers, Thomas Abida Siddiqa wrote, On 01/08/13 16:58: Thomas and Martin I have tried both suggestions. Still it did not work out. Regards Abida From: abida_sidd...@hotmail.com To: pymol-users@lists.sourceforge.net Subject: Pymol visualization problem Date: Tue, 8 Jan 2013 10:12:46 +0500 Hello, I have docked one protein named 'L1'( 450 amino acid) with another protein named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to visualize the complex. my system is windows 7 , 64 bit. The problem is, i am unable to see the sequence of 'E2' protein and so as its structure. In order to confirm, if it is docking problem or visualization problem, i have used swiss pdb viewer. it has shown me sequence and structure of both proteins. i wonder why can not i see it in pymol. secondly, i docked L1 and E2 ( this time used chain A and B of it), and visualized the complex in pymol. i was only able to see L1, and chain A of E2 (both chain A and B are alike). Then in order to see if it is docking error or visualization error, i rendered the complex in swiss pdb viwer and saw the L1 and E2 (both chain A and B). Thirdly, i changed the docking software and generated a complex using another software, this time i still was unable to visualize complete complex in pymol. Any help will be much appreciated. Kind regards Abida -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master SQL Server Development, Administration, T-SQL, SSAS, SSIS, SSRS and more. Get SQL Server skills now (including 2012) with LearnDevNow - 200+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only - learn more at: http://p.sf.net/sfu/learnmore_122512 ___ 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] Building of the Carbon lattice
Hi James,
just calculate the coordinates and write them out in PDB format, quite
simple task. Try the attached script.
Cheers,
Thomas
James Starlight wrote, On 01/04/13 09:14:
Hi Mike,
Chimera can build such lattices by means of it's build structure
module. On other hand I want to build such 2D lattices
http://imageshack.us/photo/my-images/543/lattice.png/
made from SP3 carbons as the nodes via some automatic script to
obtain lattices with desired dimensions.
James
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from numpy import array
s = 'HETATM %4d C03 UNK 1%8.3f%8.3f%8.3f 0.00 0.00 C '
c = array([[ 0.064, 2.851, -1.085 ],
[ 0.260, 1.969, 0.159 ]])
x_shift = array([ 1.67441517, -0.91605961, 1.66504574])
y_shift = array([-0.69477826, -0.40578592, 2.40198410])
out = open('lattice.pdb', 'w')
i = 0
for x in range(10):
for y in range(10):
for v in (c + (x-y/2) * x_shift + y * y_shift):
i += 1
print out, s % (i, v[0], v[1], v[2])
out.close()
try:
from pymol import cmd
cmd.load('lattice.pdb')
except ImportError:
print 'Please load lattice.pdb with PyMOL'
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Re: [PyMOL] Regarding electrostatic potential mapping
Hi Soumya, can you send me (off-list) the map file and pdb file? Cheers, Thomas Soumya Lipsa Rath wrote, On 12/29/12 13:41: Dear Users, I am trying to calculate the electrostatic potential of my protein using Delphi software. However, when I load it to pymol, I see the red colour at the centre and blue in the rest of the part even if I vary the scale. It appears to me as if it is coloring based on the distance from the centre. These are the steps after loading it to pymol: 1) load myfile.pdb 2) load myfile.phi, map 3) ramp_new e_lvl, map, 4) set surface_color, e_lvl, myfile I have attached the Delphi log file for reference also. I would really appreciate any help in this regard. Thanks, Soumya -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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] Building of the Carbon lattice
Hi Mike, I simply measured x_shift and y_shift from a cyclohexane fragment. Use the graphical Builder or the fragment command to load stuff from the fragment library. PyMOL fragment cyclohexane Cheers, Thomas Mike Marchywka wrote, On 01/04/13 15:44: Where do you get the x_shift and y_shift values? I ended up writing a program to take bond lengths and directions relative to select coord systems to generate periodic or almost periodic things. Right now polyenes but extensible. Is there some program that does this easily? This allows me to write a simple TcL script and reorient the whole molecule by changing one parameter . I don't currently have a way to include library items, like say a methyl group, and I was debating about doing this in python but I wanted to have easy access to lapack etc for later extensions. Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master HTML5, CSS3, ASP.NET, MVC, AJAX, Knockout.js, Web API and much more. Get web development skills now with LearnDevNow - 350+ hours of step-by-step video tutorials by Microsoft MVPs and experts. SALE $99.99 this month only -- learn more at: http://p.sf.net/sfu/learnmore_122812 ___ 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] which code actually executes to load axplor file? Debugstatements not executing.
Hi Mike, I guess you are on Linux with Open-Source PyMOL, right? Can you send me the xplor file that causes PyMOL to segfault? From your backtrace it looks like the problem is related to crystal symmetry information. If you want to load some format which is not yet supported by PyMOL, the easiest solution is to convert it to some already supported format on the fly and feed that to PyMOL, if possible. Cheers, Thomas Mike Marchywka wrote, On 01/02/13 17:01: I'm trying to load a self-generated xplor file and pymol keeps segfaulting. I wanted to debug the problem but can't get my debug statements to execute. The only thing that greps for xplor is a few pymol modules and plugin called edmplugin. If I rebuild the plugin and relink pymol nothing seems to change. Is this the right code? I also wanted to add a loader for other formats of density or vector fields and maybe do some rendering (I have an old viewer I wrote with glut and thought I may be able to salvage parts of that for use here). Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ 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] test for bonded atom
Hi Krisztina, I wonder if there is any way to list atoms an atom is bonded to? Use the neighbor selection operator: PyMOL select newsele, neighbor (othersele) See also: http://pymolwiki.org/index.php/Selection_Algebra I would like to list H bonded pairs but the available scritps (list_hbonds.py, or polarpairs.py) only check for distance and angle between heteroatoms, but not if any of them is actually connected to a hydrogen. As a result two carbonyl atoms are listed too. Have you also tried the distance command? It is very similar to list_hbonds/polarpairs: PyMOL distance hbonds, all, all, mode=2 There is no direct way to list these pairs, but you can use get_raw_distances script from the PyMOLWiki: http://pymolwiki.org/index.php/Get_raw_distances Hope that helps. Cheers, Thomas -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 ___ 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 not label my selection, very weird
Hi grid bird, the label command is parsed in literal mode, which means the semicolon is not recognized as command separator. Try this instead: /usr/bin/pymol -d 'fetch 1D5R, async=0; show_as cartoon; spectrum b; select t0, (resi 30); color red, selection=t0; show spheres, selection=t0; label t0, test message' -d 'save t0.pse' Cheers, Thomas grid bird wrote, On 12/20/12 17:49: Hi all, I am trying to use PyMol version 1.2r1 to do one test but I always failed to label my selection. the command line I used is the following: /usr/bin/pymol 1D5R.pdb 'show_as cartoon; spectrum b; sele t0, (resi 30); color red, selection=t0; show spheres, selection=t0; label t0, test message; save t0.pse;' I always got the error message as the following. Actually , I just want to label my selection t0 with one string message. Any ideas ? thank you. Spectrum: range ( 9.77000 to 117.74000). Selector: selection t0 defined with 7 atoms. Executive: Colored 7 atoms. File string, line 1 label=test message; save t0.pse; ^ SyntaxError: invalid syntax Label: labelled 0 atoms. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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] Memory not released after load and delete of structure
Hi Gianluigi and Martin, thanks for reporting, this is a serious issue and we are looking into it. As far as we can reproduce, it's related to the undo feature. Adding this to your scripts should help: cmd.set(suspend_undo, 1) Cheers, Thomas On Dec 21, 2012, at 9:53 AM, Gianluigi Caltabiano chimic...@yahoo.it wrote: I have the same problem since pymol 1.5, mainly with the hybrid (I can reach 10GB of ram memory with relatively small sessions). I'm on MAC OS 10.7.5 and pymol version 1.5.0.3. I had to renounce working with Hybrid unless I really need some plug-in. Gianluigi Da: Jason Vertrees jason.vertr...@schrodinger.com A: Martin Hediger ma@bluewin.ch Cc: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Inviato: Giovedì 20 Dicembre 2012 17:05 Oggetto: Re: [PyMOL] Memory not released after load and delete of structure Martin, That sounds like a memory leak in v1.3. Can you try a newer version of PyMOL and let us know if it still happens? We've fixed lots of bugs since v1.3. Also, is your script simply iterating over structures and deleting them when done? You sure you're not missing a cleanup step somewhere? (Any chance we can see the script or a stub of it?) Cheers, -- Jason On Fri, Dec 21, 2012 at 3:17 AM, Martin Hediger ma@bluewin.ch wrote: Hi Jason, I'm using PyMOL 1.3. Best regards Martin On 20.12.12 15:53, Jason Vertrees wrote: Hi Martin, Which version of PyMOL are you using? Cheers, -- Jason On Fri, Dec 21, 2012 at 1:37 AM, Martin Hediger ma@bluewin.ch wrote: Dear PyMOL users In a directory are PDB files of combined size equal to around 3MB. When I load all files into PyMOL, I observe that the required RAM of PyMOL (MacOS X 10.6) increases by roughly this amount. When I delete all objects, the RAM requirement remains the same and when I then reload all structures, the RAM requirement increases even further. I'm currently using PyMOL to batch process a number of files where a structure is loaded, modified and then deleted again from the objects list. This then results in RAM requirements of over 1GB and together with other applications, I run out of memory. Is there a way I can prevent PyMOL from behaving this way? Best regards and thanks for any help Martin -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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] setting the cutoff radius that determines when atoms are bonded
Hi Rye, only discrete objects have per state bonding information. Try this: load multistate.pdb, discrete=1 Hope that helps. Cheers, Thomas Rye Terrell wrote, On 12/05/12 18:20: I'm loading a movie file now and it appears that the bonds determined in the first frame are used throughout the entire movie, even if atoms move further apart than the cutoff. Is my perception correct here? If so, can I make the bonds be calculated for each frame? -- Thomas Holder PyMOL Developer Schrödinger Contractor -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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] Possible (minor) bug
Hi Joel, thanks for the report. This will be fixed in the next PyMOL release. Cheers, Thomas Joel Tyndall wrote, On 12/03/12 02:53: Hi Jason/all, Possible bug. When measuring distances around coordinated metals, I then wanted to change the colour of the resulting dashed line. The colour change would only appear when you turn the object off (or another). Happens with RNA and protein. Cheers J _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall Ph: +64 3 479 7293 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Keep yourself connected to Go Parallel: BUILD Helping you discover the best ways to construct your parallel projects. 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] pymol contact_map_visualizer plugin
Hi Balaji, the latest incentive builds (since v1.4, as far as I know) from Schrödinger are shipped with python 2.7. If you are looking for the open-source version, Christoph Gohlke has Windows builds with python2.7 as described on the PyMOLWiki: http://pymolwiki.org/index.php/Windows_Install#Pre-compiled_PyMOL Cheers, Thomas Ban Arn wrote, On 11/26/12 18:10: Dear Thomas Which version of pymol has python 2.7. Is it free for academics or I have to purchase license from schrodinger. Kindly advice. Many Thanks Balaji -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] morphing 3-states
Hi Jordan, morpheasy creates 30 states, which are mapped to 80 frames (forward play, pause, backward play). If you have multiple conformations, do morphs for each transition and join the results with create. Consider this example which morphs 1 - 2 - 3 - 1 # align conformations align conf2, conf1 align conf3, conf2 # do the morphs and forget about the movie frames morpheasy conf1, conf2 mstop; mset morpheasy conf2, conf3 mstop; mset morpheasy conf3, conf1 mstop; mset # append morph02 and morph03 to morph01 create morph01, morph02, 0, 31 create morph01, morph03, 0, 61 delete morph02 morph03 # if you want pauses between the morphs, use movie frames mset 1-30 30x10 30-60 60x10 60-90 Hope that helps. Cheers, Thomas On 11/25/2012 02:36 AM, Jordan Willis wrote: Hi, I have 3 different conformations of the same structure and I was wondering what is the easiest possible way to morph 3 conformations. Morpheasy works fantastic for two conformations, and this makes around 80 frames. I can then reinitialize and do the other two states. I have no idea how to link the two. Does anyone have any ideas or documentation on this? Thanks, Jordan -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries
Hi Mike, you can fetch molecular files from any web address with the load command. Examples: File type recognized from file extension: PyMOL load http://molecules.gnu-darwin.org/html/00150001_00175000/153919/153919.pdb File type given with format argument: PyMOL load http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5280443disopt=3DSaveSDF, format=sdf Also, Mobile PyMOL (for the iPad) has it's own server capabilities, including support for PubChem, PDB, Dropbox, etc. Cheers, Thomas Mike Marchywka wrote, On 11/25/12 17:26: I was trying to figure out what to eat today so naturally I started looking for PDB libraries with food components. I was looking for garlic related chemicals when I came across this, http://molecules.gnu-darwin.org/ which seems to have many pdb files. My question I guess is, what does pymol have for an API to get molecule structures from various locations or do you just have an interface for pdb.org? Besides deciding on what to eat today, I was curious if pymol has more generalized means of finding structure files. Thanks. note new address Mike Marchywka 2295 Collinworth Drive Marietta GA 30062. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] MacPyMOL 1.4 vs 1.5 problem with color
Hi Adam, this seems to be not yet fully implemented with the new shader rendering. So you may turn shaders off for now: PyMOL unset use_shaders Ray tracing is not affected, so you still can generate high quality figures with correct colors: PyMOL ray Hope that helps. Cheers, Thomas H. Adam Steinberg wrote, On 11/20/12 03:40: Hi all, If you run the script below to get a nice blob type surface (great for illustrations) in 1.4 it all works perfectly, and you can color the new map surface any color you want. If you run the same script in 1.5 it all works perfectly too, but no matter what you do you cannot change the color of the new map surface from the default white to any other color. Not via the settings, the command line, nor the gui menus. Is there a command I can add to the script below that will allow me to change the color of map surface (surfA)? or are there new commands that I should use in this script to make this work in 1.5? or is this now broken in 1.5.0.4? --- set surface_quality, 1 alter all, b=50 alter all, q=1 set gaussian_resolution,5 map_new mapA, gaussian, 1, sele or pdb, 6 isosurface surfA, mapA - Thanks in advance for the help! H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] Peptide location mapping onto protein 3D structure
Hi Sri,
if you have your structure loaded into PyMOL, you can make named
selections for your peptide sequences like this:
select pep1, pepseq RMFLS
select pep2, pepseq KGHGK
select pep3, pepseq ALSDL
There are also scripts available for pattern matching, for example:
http://pymolwiki.org/index.php/FindSeq
Highlighting the selections with colors:
color white
color red, pep1
color blue, pep2
color green, pep3
You can query these selections on various properties:
# (approximate) surface area
set dot_solvent
get_area pep1
# secondary structure
print [a.ss for a in cmd.get_model('pep1 and name CA').atom]
Doing this on a large number of structures is possible if you write a
python script, which requires general programming skills. All the
commands shown above are accessible from the PyMOL python API. Examples:
from pymol import cmd
cmd.select('pep1', 'pepseq RMFLS')
cmd.color('red', 'pep1')
print cmd.get_area('pep1')
Hope that helps.
Cheers,
Thomas
Sri Ramarathinam wrote, On 11/22/12 08:16:
Hi All
I am very new to using Pymol. I am wondering if anyone can point me towards
the right direction with the following:
1) I have a list of peptides and would like to know what their location is on
their respective proteins which already have structures in PDB (surface
exposed, buried, helix, loop or beta sheet?)
I guess I could do it manually but the peptide list could go into
hundreds and would be nice to see if there a command line or a script I could
use.
2) Can i ask Pymol to show the peptide's location on the 3d structure of the
protein? perhaps in a different colour to highlight location?
Manually I would select on the sequence and show as whatever I want but
is there a command to automate a huge list?
Is it possible to do these tasks with Pymol or is there any other software I
could be using?
Thanks very much for your help,
Cheers
Sri
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
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Re: [PyMOL] Controlling colors in volume object
Hi Per, you may check the volume_esp function here: https://github.com/speleo3/pymol-psico/blob/master/psico/electrostatics.py As Jason said in that earlier thread, the volume API is work in progress and will probably change soon. Cheers, Thomas Per Larsson wrote, On 11/21/12 19:01: Following up myself on this. I did some more digging on Google, and putting together bits and pieces this is what I have currently. It works, but does not (yet) allow me to scale the colors according to eg. the max and min values of my density (which I do not know how to access). I guess that means I have a new question about accessing details about the density-object. Thanks /Per load density.dx, d cmd.volume(density,d,1.0) bg_color white from pmg_tk.skins.normal.ColorRampModel import ColorRamp r = ColorRamp(nColors=256) r.addColor(0,(0,0,0,0),0) r.addColor(2,(0.39,0.67,1,0.01),0) r.addColor(130,(0,1,0.50,0.25),0) r.addColor(192,(1,0.0,0.0,0.25),0) r.addColor(255,(1,0,0,0.25),0) ramp_colors = r.getRamp() cmd.volume_color(density,ramp_colors) 21 nov 2012 kl. 17:30 skrev Per Larsson: Hi pymol-users I have previously been able to make quite nice visualizations of my volume object, containing the time-averaged density of atoms from a MD-simulation. For making even more improvement, I'd like to be able to use a script (either python or pml) to control which regions of density gets which color. I've found this thread http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10294.html that suggests it to be possible, but understanding how to use that for my case is unfortunately (yet) a bit beyond my current pymol-skills. Ideally I would want to have a solution that allows me to load in my volume-file (in .dx format), assign colors to different regions of density systematically (the Volume-GUI is great, but somewhat tricky to make quick changes with), and display the result on screen. Is such a thing possible? Thanks /Per -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] assigning secondary strux to artificial AAs
Hi Jonny, I think it should be sufficient to have the atom names along the backbone correct (CA, N, C) and to have increasing residue numbering. If you like you can send me your file and I'll have a look. Cheers, Thomas Johnny Pham wrote, On 11/15/12 09:41: Hi, I was wondering if I have unnatural amino acids in beta sheet mimicking peptides, is there a way to have them show up as a beta sheet in the cartoon representation? I understand the code: alter 1-11/, ss='S' as an example of assigning residues 1-11 as a beta sheet but how do I tackle artificial amino acids. Thanks! -Johnny -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] fuse two proteins by a peptide bond
Hi Sheng, you can do this interactively in Editing Mode. Choose Mouse 3 Button Editing from the menu or click the lower-right panel in the main window. In Editing Mode, you can pick single atoms into named selections (pk1, pk2, ...). So for your peptide bond, pick the N and the C, type fuse and hit enter. To adjust the torsion angle, you can CTRL+Drag with the left mouse button. If you want to fuse non-interactively (using a script), you can select the endpoint atoms using PyMOL's powerful selection language: PyMOL fuse last (obj01 and name C), first (obj02 and name N) Hope that helps. Cheers, Thomas Sheng wrote, On 11/19/12 02:55: Dear,all I'm a new user. I wonder how to fuse two proteins by a peptide bond using pymol ? (from 2 .pdb files into 1 file) I found the following description in user manual.but I don't know how to select a single atom. I know it sounds silly, but I really don't know how to do this step. I really appreciate your help! -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] Field lines representation
Hi Quentin, this is called gradient in PyMOL. Just load your map into PyMOL and then click A gradient default or use the gradient command on the command line. Hope that helps. Cheers, Thomas On 11/16/2012 08:20 AM, Quentin Delettre wrote: Dear Pymol users, I would like to know if there is a way to display field lines in the same way that vmd does. I know that pymol APBStools2 plugin offer the possibility to display field lines but it's too complex compared to vmd style. (see http://www.ks.uiuc.edu/Research/vmd/current/ug/node77.html and http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-vmd ) Thanks. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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 certain residues within X angs of a point/residue
Hi John, here is something to start with: # put everything in state 1 (convert states to objects) split_states capsid delete capsid # specify the fixed residue select fixedresidue, capsid_0001 and chain D and resi 30 # select residues of interest within given radius select s1, chain A+B+C and resi 23+45+46 select s2, s1 within 40 of fixedresidue # highlight result color blue color yellow, s2 See also: http://pymolwiki.org/index.php/Selection_Algebra#Comparison_of_distance_operators Cheers, Thomas On 11/15/2012 10:47 AM, Jonathan Grimes wrote: i am wanting to highlight a number of residues on a virus capsid. i have 60 states (objects), and wanted to only select particular residues (say resi 23,45,46 from 3 chains across all 60 objects) that are within say 20A or 40A from a fixed point (or residue). could i get advice on what scripts i could use/edit to get this done. thanks jon Dr. Jonathan M. Grimes, NDM Senior Reseach Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] Fwd: contact_map_visualizer pymol plugin
Hi Balaji, you need to upgrade your PyMOL installation. The 0.99rc6 version has a quite old version of python build-in and does not use your python-2.7 installation. Cheers, Thomas On 11/14/2012 06:58 AM, Ban Arn wrote: Dear Pymol Users I am using pymol v-0.99rc6 (in windows). I'm trying to install and work on the contact_map_visualizer.py plugin. I am using python-2.7and installed all dependecies as mentioned in the plugin site. Initially, I had image module error and later looking into the link http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10289.html; I sorted out the above error. I installed the script using plugin and getting the following error *Exception in plugin 'Contact_Map_Visualizer' -- Traceback follows...* *Traceback (most recent call last):* * File C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\PMGApp.py, line 156, in initialize_plugins* *__builtin__.__import__(mod_name)* * File C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\Contact_Map_Visualizer.py, line 291* * finally:* * ^* * SyntaxError: invalid syntax* *Error: unable to initialize plugin Contact_Map_Visualizer* I tried running the script using the command lines run contact_map_visualizer.py contact_map_visualizer test.png and its shows the same error *PyMOLrun contact_map_visualizer.py* *Traceback (most recent call last):* * File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py, line 285, in parse* *parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names)* * File C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py, line 407, in run_file* *execfile(file,global_ns,local_ns)* * File contact_map_visualizer.py, line 291* * finally:* * ^* * SyntaxError: invalid syntax* Could you please help me to sort out this error. Kindly advice. Many Thanks Balaji -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ 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] Angle between two structure upon alignment
Hi Appu, if I understand you correct then you have a structure with at least two domains. If you align two conformations of that structure, one domain does not get superposed nicely. Right? The psico module provides the command angle_between_domains, which is what you are looking for I guess. Example: (tilted domain spans residues 100 to 150) PyMOL align s1, s2 PyMOL select d1, s1 and resi 100-150 PyMOL select d2, s2 and resi 100-150 PyMOL angle_between_domains d1, d2 This requires numpy and psico installed. Download psico: https://github.com/speleo3/pymol-psico Hope that helps. Cheers, Thomas Appu kumar wrote, On 11/01/12 04:50: Dear user Can you please help me in finding the angle between two structure upon alingment. I have aligned two structure and one structure is not perfectly aligned on other. There is domain of two structure tilting outward upon alignment. IS there any way to find the angle between two structure. Thanks in advances. -- 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_sfd2d_oct ___ 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] visualise NOEs
Hi Krisztina, check the attached script (strongly modified). It doesn't use a regex anymore, but uses a split function which takes parentheses into account. Also it doesn't parse name and resi, but passes the selection string directly to PyMOL (which understands most of CNS selection syntax!). Your example selects segidA, since PyMOL will strip off whitespace from the segid, you might need something like this to fix it before calling plot_noe: PyMOL alter all, segi=segi.rjust(4) Hope that helps. Cheers, Thomas On 10/31/2012 04:36 PM, Krisztina Feher wrote: Dear All thanks to Thomas for the modfication on the plot_noe.py. It turns out that the CNS .tbl file can have different formats, the one I used only includes residue ID and atom name, but soemtimes it also inlcudes segment ID as well, see on the attached file. How do I have to modify the noe_regex pattern so that it is recognised? Thanks in advance, regards, Krisztina -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen plot_noe.py Description: application/chimera -- 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_sfd2d_oct___ 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] visualise NOEs
Hi Krisztina, I slightly modified the script, see attachment. The regular expression is modified and I replaced search by match. The script could be further optimized (exception handling etc.) but with your example file it works fine now. Cheers, Thomas On 10/29/2012 04:06 PM, Krisztina Feher wrote: Sure, thanks for looking at it! Krisztina --- On *Mon, 10/29/12, Thomas Holder wrote: From: Thomas Holder spel...@users.sourceforge.net Subject: Re: [PyMOL] visualise NOEs To: Krisztina Feher feher_kriszt...@yahoo.com Date: Monday, October 29, 2012, 4:04 PM Hi Krisztina, can you send me the restraints file and PDB file as well? Cheers, Thomas On 10/29/2012 04:00 PM, Krisztina Feher wrote: Hi Thomas, thanks a lot for your reply! Now I was running the script from command line and executed it: it did not display anything on the structure. I inserted a couple of print statements into the script (attached), but it seems that the noe_regex is not being found in the variable line by the .search method (see the output below: match is None). The pdb file does have residue 433 and all the listed atom names. The noe_regex looks sort of complicated, I have no idea how to fix it. If anyone had an idea how to fix it, I would very much appreciate it. Thanks, Krisztina ps. If this script works for on your system, please write me too! -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen plot_noe.py Description: application/chimera -- The Windows 8 Center - In partnership with Sourceforge Your idea - your app - 30 days. Get started! http://windows8center.sourceforge.net/ what-html-developers-need-to-know-about-coding-windows-8-metro-style-apps/___ 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] red_white_blue palette color bar
Hi Yamei, you can create a dummy color ramp: PyMOL ramp_new colorbar, none, [-5, 0, 5], [red, white, blue] There is also the spectrumbar script: http://pymolwiki.org/index.php/Spectrumbar Cheers, Thomas Yamei Yu wrote, On 10/29/12 16:46: Hi all, Do any know how to generate a color bar for red_white_blue? Thank you very much! yamei -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- The Windows 8 Center - In partnership with Sourceforge Your idea - your app - 30 days. Get started! http://windows8center.sourceforge.net/ what-html-developers-need-to-know-about-coding-windows-8-metro-style-apps/ ___ 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] Custom menus and shortcuts?
Hi Boris, Boris Kheyfets wrote, On 10/23/12 19:28: [...] But I want bk_hides_W to be a toggler. So I need a way to set a state of my defun. If I do def bk_toggles_W (): Hides W molecules. if cmd.get(bk_toggles_W): cmd.hide(all) cmd.show(spheres, not (resn W)) cmd.set(bk_toggles_W, 0) else: cmd.show(spheres, resn W) cmd.set(bk_toggles_W, 1) pymol is upset -- I think it is because it doesn't know bk_toggles_W setting: If you need a global variable, use pymol.stored: from pymol import stored stored.bk_toggles_W = 0 def bk_toggles_W (): Hides W molecules. if stored.bk_toggles_W: cmd.hide(all) cmd.show(spheres, not (resn W)) stored.bk_toggles_W = 0 else: cmd.show(spheres, resn W) stored.bk_toggles_W = 1 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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_sfd2d_oct ___ 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 rotate entire section of structure relative to rest
Hi Alex, sculpting is not the right tool for your task. PyMOL has all the basic editing features like rotating around a bond etc. Enter Editing mode, pick a bond with the mouse and rotate around the bond by pressing CTRL and click-dragging a second atom. You can enter Editing Mouse Mode by clicking on the lower-right panel. Hope that helps. Cheers, Thomas On 22.10.2012 22:27, Alex Truong wrote: Hi All, I'm relatively new to this software, and even though I've been using it for a few months, I haven't really had to use some of the more advanced options yet. This would be my first foray into actual manipulation. That being said, I'm trying to figure out how to move a small section at the N-terminus of my protein while keeping the rest static. That is, I'd just like to be able to rotate one bond and fix the relative positions and structures of the entire rest of the protein. I did some googling, and there was something about a Sculpting feature, but when I tried it, sections lit up that I was not interested in, and I was basically moving tiny sections at a time without preserving the structures I wanted. Is there a way to just manipulate the angle so I can swing that section out and away from its current position? I'll deal with the positions of those individual residues if this cannot method cannot resolve my problem. Thanks, Alex -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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_sfd2d_oct ___ 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] Tab completion using object names, not filesystem files?
Hi Ron,
tab completion is controlled by the cmd.auto_arg variable, which is a
list of dictionaries.
http://pymolwiki.org/index.php/auto_arg
For all arguments which do not have an entry in auto_arg, the default is
to auto-complete file names. For your purpose you need to define
something like this:
python
import glob
cmd.auto_arg[0]['save'] = [
lambda: cmd.Shortcut(cmd.get_names() + glob.glob('*')),
'filename or object name', '']
python end
Cheers,
Thomas
Ron Jacak wrote, On 10/17/12 22:25:
PyMOL-users,
I'm wondering if there's a way to make the tab completion engine use
the currently loaded (or visible) object names rather than (or in
addition to) the files in the filesystem? I usually have sessions
with very long object names that I want to include in custom selection
expressions and the tab completion doesn't work because oftentimes the
PDB files are not in the same directory as the session. I found the
function complete() in modules/pymol/parsing.py that seems to be what
figures out how to complete the command that's been entered. I think
if I just added a list of the currently loaded objects to the list
obtained by globbing the filesystem, it would do what I'm looking for.
Any ideas on the best way to do that?
Best,
-Ron
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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Re: [PyMOL] Make sure zoom is viewed from surface
Hi Troels, Jason, Edward,
nice little problem and nice layouts by Jason and Edward. Let me
contribute some code, it follows Edwards approach.
See attachment. Requires psico.
Cheers,
Thomas
Edward A. Berry wrote, On 10/08/12 20:57:
Jason Vertrees wrote:
Hi Troels,
I've run into this problem a few times, too, but never took the time
to solve it correctly.
A quick plan might look like:
* cmd.orient on the selection
* store the view vector (http://www.pymolwiki.org/index.php/Get_View)
* let C1 = count the number of atoms behind the view vector, using
something like (http://www.pymolwiki.org/index.php/SelInside)
* invert the view vector
* let C2 = count the number of atoms behind the view vector, using
something like (http://www.pymolwiki.org/index.php/SelInside)
* compare C1 to C2, choosing the
* if C2 C1 then flip the view
You could use other tricks. I'm sure the community has other ideas.
Calculate center of mass or average of all coordinates
calculate vector from that to point of interest
rotate view so that vector points toward front/camera
translate so point of interest is centerd
maybe reverse the last two steps?
Cheers,
-- Jason
On Sun, Oct 7, 2012 at 10:04 AM, Troels Emtekær Linnet
tlin...@gmail.com wrote:
Hi pymolers.
I am generating a list of residue ID's from some calculations.
Now I want to make a little script that select the residue and sticks it
and then zoom and make .png file.
How do I make sure that the zoom, is viewed from outside the protein for
each residue/.png file?
Best
Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
from pymol import cmd, CmdException
def zoomoutside(selection, ref='', state=-1, operator='byobject',
quiet=1, **kwargs):
'''
DESCRIPTION
Zoom the given selection and orient such that the object center of
mass is behind the selection center of mass.
USAGE
zoomoutside selection [, ref [, state ]]
ARGUMENTS
selection = string: atom selection to zoom on
ref = string: reference selection to orient behind selection
{default: byobject selection}
SEE ALSO
zoom, orient
'''
from chempy import cpv
from psico.querying import centerofmass
state, quiet = int(state), int(quiet)
if not ref:
ref = '%s (%s)' % (operator, selection)
com_sele = centerofmass(selection, state)
com_ref = centerofmass(ref, state)
view = list(cmd.get_view())
camera_rotation = [view[0:3], view[3:6], view[6:9]]
vec = cpv.sub(com_sele, com_ref)
vec_camera = cpv.transform(camera_rotation, vec)
axis = cpv.cross_product(vec_camera, [0.,0.,1.])
angle = cpv.get_angle(vec_camera, [0.,0.,1.])
rotation = cpv.rotation_matrix(angle, axis)
view[:9] = [x
for row in cpv.multiply(rotation, camera_rotation)
for x in row]
cmd.set_view(view)
cmd.zoom(selection, state=state, **kwargs)
cmd.extend('zoomoutside', zoomoutside)
--
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Re: [PyMOL] bond connection file
Hi Vishwas, atom connectivity is the same for all states unless you have a discrete object. Try this: PyMOL set connect_mode, 1 PyMOL load file.pdb, discrete=1 Cheers, Thomas Vishwas Vasisht wrote, On 10/05/12 08:59: Hi Thomas, Thanks, it works for single frame. But when I use multiple frame (using MODEL and ENDMDL), the connections which i specified in the first frame is retained for rest of the frames. Am I doing some mistake in the way I wrote my PDB file? Regards Vishwas 2012/10/4 Thomas Holder spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net 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] 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] PyMOL Model player
Hi Martin, the player cannot run backwards, but you can map states in reverse order to movie frames with mset. Or choose from the menu: Movie Program State Sweep Or use the corresponding command: cmd.movie.add_state_sweep(pause=0) Hope that helps. Cheers, Thomas On 10/02/2012 02:31 PM, Martin Hediger wrote: Dear PyMOL Users Is it possible to let the PyMOL model player go back and forward, instead of jumping from the end to the start, once it reached the last loaded model of an object? Thanks for hints. Martin -- 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] Doubt with using APBS electrostatics in PyMOL
Hi Mohan, can you please provide some more information, like: * what parameters did you choose on the website * what representation in PyMOL did show the distorted structure * was that a public available PDB structure so that we could try to reproduce your result Does it help if you check Add/keep chain IDs in the PQR file with the PDB2PQR Server? If your structure has multiple chains, then PyMOL will show incomplete cartoon representation if the chain ids are missing. You can also try: PyMOL set retain_order PyMOL load file.pqr Cheers, Thomas Mohan Pradhan wrote, On 10/02/12 18:36: Hi When I load the pqr file of the structure in PyMOL for creating the electrostatic surface using APBS, I see the distorted structure. I have generated this site using the PDB2PQR module at http://nbcr-222.ucsd.edu/pdb2pqr_1.8/ Can someone explain why it is so. -- 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] Adding hydrogens
Hi Martin, do you have retain_order set to 1? This is not the default. Try: unset retain_order save file.pdb Cheers, Thomas Martin Hediger wrote, On 09/25/12 18:24: Dear PyMOL list I'm adding hydrogens to a crystal structure. Upon saving, however, I realize all hydrogens have been added to the beginning of the PDB file. Can PyMOL be configured such that the hydrogens are placed at the intuitively appropriate place in the PDB file? Thanks for any hints. Martin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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] Label entire movie
Hi Anke, Rasbach, Anke wrote, On 09/24/12 13:08: [...] Is it also possible to change font and box color? no, that's not possible. The colors are hard-coded. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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] Label entire movie
Hi Anke, you can use the message wizard to place a text box to the upper left corner of the viewport. PyMOL wizard message, Some free text Cheers, Thomas Rasbach, Anke wrote, On 09/21/12 13:35: Hi everyone, we have generated a quite complex pymol movie and would like to include a label that is always located in the lower right corner throughout the entire movie. We have already labeled a pseudoatom positioned at the lower right corner but due to camera motions the text is flying around as well. Is there the possibility of adding a global text box not specified to a x,y,z position? Or an easy way to move the pseudoatom accordingly? Thanks Anke -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Got visibility? Most devs has no idea what their production app looks like. Find out how fast your code is with AppDynamics Lite. http://ad.doubleclick.net/clk;262219671;13503038;y? http://info.appdynamics.com/FreeJavaPerformanceDownload.html ___ 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] question
Hi Mona, I am very interested to here if it is possible to align a stick structure with a cartoon strucrture in Pymol? structure alignment is independent of visual representation. So yes, you can align a stick structure to a cartoon structure. Is it possible to put the short aa code or name in the peptide structure in pymol? you can add labels to atoms. So to label each residue with its name (resn), just label all CA atoms: PyMOL label name CA, resn Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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] movie help, rotating around an objects own center of mass.
Hi Jordan, the rotate command has a camera argument. Does it help if you set that to zero? rotate [0,0,1],360, object=3hmx_ant, origin=3hmx_ant, camera=0 Cheers, Thomas Jordan Willis wrote, On 09/17/12 02:55: Hello, I'm making a movie, and I think I really got it down! However, I'm having trouble with independent rotations. I have nine independent objects, of which three I'm trying to get to rotate their own z-axis. Is this possible? Let me show you what I mean :) frame 30 rotate [0,0,1],360, object=3hmx_ant, origin=3hmx_ant rotate [0,0,1],360, object=2b1a_ant, origin=2b1a_ant rotate [0,0,1],360, object=2xwt_ant, origin=2xwt_ant #store all views mview store, object=2b1a_ant mview store, object=2b1a_h mview store, object=2b1a_l mview store, object=2xwt_ant mview store, object=2xwt_h mview store, object=2xwt_l mview store, object=3hmx_ant mview store, object=3hmx_l mview store, object=3hmx_h #reinterpolate mview reinterpolate, object=2b1a_ant mview reinterpolate, object=3hmx_ant mview reinterpolate, object=2xwt_ant The problem is that the rotate command uses the entire scenes y-axis rather than the objects. I understand you can supply an axis vector, but I have no idea how to do this. Essentially I want to do what movie.roll would do, but just to one object independently of the entire scene. Jordan -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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] movie help, rotating around an objects own center of mass.
Hi Jordan,
I guess you actually do want the axis in camera space, not in object
space. Unfortunately the origin argument will pick the origin of object
coordinate space and not it's geometric center.
Check the attached script, which I modified slightly. I defined a
my_rotate command which takes care of the origin.
Hope that helps.
Cheers,
Thomas
Jordan Willis wrote, On 09/17/12 18:13:
Hi Thomas,
I was crazy not to see that option. Although it did change the axis,
it is not using the objects axis, but an unidentified axis I can't
quite put my finger on. By changing the origin= option, it does not
seem to have an effect. Is it possible that I'm putting the wrong
command into the origin option?
If you would like to look, my .pml file and the pdbs I loaded I have
attached. I guess I still can't figure out how to use the selected
objects center of mass. Any help would be much appreciated!
Thanks, Jordan
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
reinitialize
set matrix_mode, 1
set movie_panel, 1
set scene_buttons, 1
set cache_frames, 1
set movie_auto_interpolate, off
config_mouse three_button_motions, 1
python
import glob, os
path = /Users/jordanwillis/workspace/specificaim3/msd_movie/files/
if not os.path.exists(path):
path = 'files/'
l1 = glob.glob(path+*A*.pdb)
l2 = glob.glob(path+*B*.pdb)
l3 = glob.glob(path+*C*.pdb)
for j in l1[:10]:
cmd.load(j,A1)
for g in l2[:10]:
cmd.load(g,B1)
for d in l3[:10]:
cmd.load(d,C1)
cmd.load(path+2b1a.pdb, A_bb)
cmd.load(path+2xwt.pdb, B_bb)
cmd.load(path+3hmx.pdb, C_bb)
try:
from psico.querying import centerofmass
except ImportError:
centerofmass = lambda s: [(a+b)/2 for (a,b) in zip(*cmd.get_extent(s))]
def my_rotate(angle, object, axis='y'):
com = centerofmass(object)
cmd.rotate(axis, angle, object=object, origin=com)
cmd.extend('my_rotate', my_rotate)
python end
bg white
hide lines
#object creators
create 2b1a_ant, A_bb and chain P
create 2xwt_ant, B_bb and chain C
create 3hmx_ant, C_bb and chain A
create 2b1a_l, A_bb and chain L
create 2xwt_l, B_bb and chain B
create 3hmx_l, C_bb and chain L
create 2b1a_h, A_bb and chain H
create 2xwt_h, B_bb and chain H
create 3hmx_h, C_bb and chain H
set_view (\
-0.987339199, -0.147254646,0.058693748,\
-0.130136862,0.541538239, -0.830523551,\
0.090512969, -0.827677608, -0.553851545,\
0.000551268,0.000143198, -327.257324219,\
21.386798859, -23.021564484, 12.119427681,\
176.506362915, 478.079681396, -20.0 )
### cut above here and paste into script ###
select antigens, chain C + chain A + chain P
select light, chain B + chain L
select msd_residues, A1 + B1 + C1
select heavy, not msd_residues and chain H
deselect
color grey20, heavy
color forest, antigens
color sand, light
spectrum b, blue_white_red, msd_residues
#show sticks, msd_residues
show surface, 2b1a_ant + 2xwt_ant + 3hmx_ant + 2b1a_l + 2xwt_l + 3hmx_l +
2b1a_h + 2xwt_h + 3hmx_H
show cartoon, 2b1a_h + 2xwt_h + 3hmx_h
set transparency, .5
translate [-60,0,0], object=2b1a_ant
translate [-60,0,0], object=2b1a_h
translate [-60,0,0], object=2b1a_l
translate [60,0,0], object=3hmx_ant
translate [60,0,0], object=3hmx_l
translate [60,0,0], object=3hmx_h
mset 1 x160
frame 1
color magenta, antigens
mview store, object=2b1a_ant
mview store, object=2b1a_h
mview store, object=2b1a_l
mview store, object=2xwt_ant
mview store, object=2xwt_h
mview store, object=2xwt_l
mview store, object=3hmx_ant
mview store, object=3hmx_l
mview store, object=3hmx_h
frame 40
translate [0,10,0], object=3hmx_ant
translate [0,10,0], object=2b1a_ant
translate [0,10,0], object=2xwt_ant
mview store, object=2b1a_ant
mview store, object=2b1a_h
mview store, object=2b1a_l
mview store, object=2xwt_ant
mview store, object=2xwt_h
mview store, object=2xwt_l
mview store, object=3hmx_ant
mview store, object=3hmx_l
mview store, object=3hmx_h
frame 50
color forest, antigens
color magenta, light
#translate [0,-10,0], object=3hmx_ant
#translate [0,-10,0], object=2b1a_ant
#translate [0,-10,0], object=2xwt_ant
my_rotate 180, 3hmx_ant
my_rotate 180, 2b1a_ant
my_rotate 180, 2xwt_ant
#,origin=3hmx_h
#rotate [0,0,1], 180,object=2b1a_ant,camera=0,origin=2b1a_ant
#rotate [0,0,1], 180,object=2xwt_ant,camera=0,origin=2xwt_ant
mview store, object=2b1a_ant
mview store, object=2b1a_h
mview store, object=2b1a_l
mview store, object=2xwt_ant
mview store, object=2xwt_h
mview store, object=2xwt_l
mview store, object=3hmx_ant
mview store, object=3hmx_l
mview store, object=3hmx_h
frame 90
translate [-10,0,0], object=3hmx_l
translate [-10,0,0], object=2b1a_l
translate [-10,0,0], object=2xwt_l
mview store, object=2b1a_ant
mview store, object=2b1a_h
mview store, object=2b1a_l
mview store, object=2xwt_ant
mview store, object=2xwt_h
mview store, object=2xwt_l
mview store, object=3hmx_ant
mview store, object=3hmx_l
mview store, object=3hmx_h
frame 100
color sand, light
Re: [PyMOL] Question about mutagenesis wizard
Hi Maurício, what you describe here is called homology modeling. Although PyMOL has some modeling capabilities, I'd strongly recommend to use a real homology modeling tool such as MODELLER to do this. http://salilab.org/modeller/ Hope that helps. Cheers, Thomas Maurício Menegatti Rigo wrote, On 09/14/12 19:44: Dear Pymol users, I'm a begginer with command lines in Pymol. I'm trying to complete the following task through a pymol script: 1) Write a file named file1.txt with an aminoacid sequence (e.g. CVGLTUW) 2) Open a .pdb molecule (file2.pdb) with the same number of residues, but with a different sequence (e.g. ALTWSIK) 3) Write a code where the pymol will pick each residue of the file2.pdb (I believe that this could be made by the mutagenesis wizard command) and mutate for the respective aminoacid written in my file1.txt 4) Save the new filein .pdb format (file3.pdb) I'll be very greatful for any help! Thanks in advance, -- M.Sc. Maurício Menegatti Rigo Núcleo de Bioinformática do Laboratório de Imunogenética Departamento de Genética Instituto de Biociências Universidade Federal do Rio Grande do Sul - Campus do Vale Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M CEP:91501-970 Caixa Postal 15053 Porto Alegre, RS, Brasil Tel: +55 51 3308 9938 tel:%2B55%2051%203308%209938 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Got visibility? Most devs has no idea what their production app looks like. Find out how fast your code is with AppDynamics Lite. http://ad.doubleclick.net/clk;262219671;13503038;y? http://info.appdynamics.com/FreeJavaPerformanceDownload.html ___ 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 create a custom rainbow according to residue number
Hi Afonso, this should do the job: http://pymolwiki.org/index.php/Spectrumany Example: PyMOL run spectrumany.py PyMOL spectrumany resi, lime green forest, chain A+C+E PyMOL spectrumany resi, lightblue blue density, chain B+D+F Hope that helps. Cheers, Thomas Afonso Duarte wrote, On 09/04/12 15:15: Dear All, I'm using Pymol1.4 in windows and I have a protein build-up by 6 domains organized in pairs in an anti-parallel fashion ( i.e. if A and V are the domains: AV AV AV) (the domains are structurally homologous but the sequence is different). I want to color the two domains in different colors (i.e. A green and V blue) but then I want this colors to be in a gradient according to the sequence (i.e. A should be colored from light green to dark green and V colored from light blue to dark blue). As I understood one cannot create new color schemes in the spectrum command (if yes I would just color them individually) am i right? For that reason I'm thinking of creating a ramp that I would color with that color scheme, for this i need to create a selection containing the residue number of the residues involved. Is there a way to directly create a list of residue number in Pymol ? Best Afonso ### Afonso Duarte ITQB-UNL Portugal -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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] PyMOL Visualization Query
Hi Spyros,
so you want to visualize how often each atom matches your GREP query?
You could put that count number as b-factor and then do a spectrum
coloring. Example:
python
# load one of the homology models
cmd.load('tem1_mod445.pdb')
# set b-factor to zero for all atoms
cmd.alter('all', 'b=0')
# increment b-factor for each GREP line
for line in open('output.txt'):
line = line.split(':', 1)[-1]
name = line[12:16]
resi = line[22:26]
cmd.alter('resi %s and name %s' % (resi, name), 'b=b+1')
# show spheres, colored from yellow to red according to count
cmd.show_as('spheres')
cmd.spectrum('b', 'yellow_red', quiet=0)
python end
Cheers,
Thomas
Spyros Charonis wrote, On 08/31/12 17:21:
Dear PyMOL community,
I have a python script that reads a directory of ~500 homology models
generated from a pipeline (I used a PDB file as a template to generate
the models).
It extracts residues that have charge-bearing atoms on them. When using
GREP/EGREP to query a specific coordinate (e.g. 29.010) against the dataset
and to determine which and in how many homology models it is present,
the output looks like so:
./tem1_mod445.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010
./tem1_mod446.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010
./tem1_mod461.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010
./tem1_mod179.pdb:ATOM NZ LYS A 151 -12.607 8.920 29.049
./tem1_mod180.pdb:ATOM NZ LYS A 151 -12.607 8.920 29.049
and so forth.
The ./tem1_mod string refers to the specific homology model file
that contains the atom.
QUESTION
Once I have collected all atoms that I possess z-coordinates values
within a range (29 - 54), Is there a way to map these onto a template PDB
structure (in my case 3NY8 - adrenergic receptor). In other words,
having collected hundreds of atomic coordinates (all from charged
residues and
all with z-values between 29.000 - 54.000 angstroms) across several
different homology models (my dataset contains ~500 models)
is there a way to visualize (using the z-coordinate spatial value as the
criterion) them on a single PDB file?
The reason I would like to do this is to observe any patterns in the
occurrence of charge throughout the transmembrane region of receptor
proteins.
Many thanks in advance.
Regards,
Spyros Charonis
--
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MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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Re: [PyMOL] colouring states independently
Hi John,
what you need is a discrete object, not only because of the coloring,
but also because you say the number of particles is not the same for
each state.
Try to apply two modifications:
1) discrete argument for load:
cmd.load(file, movie, discrete=1)
2) state argument for select:
cmd.select(particle, id +str(particle_index+1), state=i)
I hope this will work :)
Cheers,
Thomas
John Russo wrote, On 08/31/12 09:14:
Hi,
I have been fighting with this problem for some time now,
and I think it is time to try to ask to more experienced users.
What I want to achieve is really simple. I want to make a movie
with only spheres. At every frame each sphere has also a scalar
property (e.g. local density) which is used to color the sphere
accordingly.
So my input are a series of xyz files, and a corresponding series
of files holding the value of that scalar for each particle.
What I'm doing now is:
*) loading all the xyz file into different states
*) creating a frame from each of these states
*) loop on the different frames and color the spheres
according to the field
My problem is in this last point, as I cannot find a way to
tell pymol to colour each sphere only for that frame, and
I always end up with a movie where the colour of the spheres
is fixed by the last frame.
Here is some pseudo code for what I'm doing:
for file in file_list:
cmd.load(file,movie)
cmd.mset(1 -%d % cmd.count_states())
for i in range(1,cmd.count_states()+1):
name=%d % (i)
cmd.frame(i)
scalar=readField(scalar_field[i])
for particle_index,s in enumerate(scalar):
cmd.select(particle,id +str(particle_index+1))
cmd.color(custom_color[s],particle)
cmd.scene(name,store)
cmd.mview('store',name)
One last thing, the number of particles is not the same for every state.
I hope somebody can help me. Thanks,
John
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
--
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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
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Re: [PyMOL] APBS problem
Hi Warren, run pdb2pqr with the --whitespace argument to make sure the columns are separated with whitespace. If you still want to adjust the coordinates, you can use the alter_state command in PyMOL. alter_state 1, all, (x,y,z)=(x+100,y+100,z+100) http://www.pymolwiki.org/index.php/Alter_State Cheers, Thomas Warren Gallin wrote, On 08/30/12 06:54: Hi, I am having trouble running APBS on a structure, and it appears to be because some of the coordinates are -100 or more negative. This leads to APBS reading numbers from adjacent columns as concatenated strings because there is no space between the columns. This is happening either if I use the plugin or run PDB2PQR and APBS as stand-alone applications. If I can adjust the co-ordinates such that the relative positions of the atoms do not change but the coordinates stay greater than -100 I think that the problem would be solved. Has anyone ever encountered this problem, and is there a simple solution in PyMol to adjust the coordinates and then save a simple PDB file with the corrected values? Thanks, Warren Gallin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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] pymol plugin with subprocess thread
Hi Ed, you need to put 2# and 3# into the function foo() and call foo_async(). If you like you can send me your plugin and I'll have a look at it. Cheers, Thomas Mister Vanhalen wrote, On 08/28/12 18:02: Many thanks for you answer Thomas! But I feel I didn't explained clearly my problem. With your code, my problem is now to know when my program finished. My plugin is organized like that : 1 # here it is the main of the plugin 2 # launch of my external program 3 # treatment of result of program to load new structure in PyMoL This part has to wait the end of program. If I wait - I can use PyMoL and If I put in daemon it will be execute without result of my program So my question is to know how can I wait the result of my program but with the possibility to use PyMoL. And when it is finished, to go on lines programming in the plugin... Thank you again for your help, Ed' On Tue, Aug 28, 2012 at 5:48 PM, Thomas Holder spel...@users.sourceforge.net mailto:spel...@users.sourceforge.net wrote: Hi Ed, this is possible. Example: def foo(a, b, c): command = ./myprogramm arg1 arg2 process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) process.wait() def foo_async(a, b, c): import threading t = threading.Thread(target=foo, args=(a, b, c)) t.setDaemon(1) t.start() Hope that helps. Cheers, Thomas Mister Vanhalen wrote, On 08/28/12 17:33: Hi PyMoLers, I need to launch an external program through a plugin. When I launch my program by my button in my interface (the plugin) through this usual code : command = ./myprogramm arg1 arg2 process = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) process.wait() PyMol waits the end of the program to screen a windows with my result and load new structure and cgo in PyMol, that's normal. Is it possible that PyMol can go on and only when my program has finished, my plugin screens the results and load new structure in PyMoL. I would like that we can use PyMoL in the meantime that my program is running. Is it possible? I don't know how to put the thread for that... Thank you for your help, Ed' -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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] Ca sphere size from b-factor value
Hi Doug, scaling to the range of observed values: stored.b = [] iterate n. CA, stored.b.append(b) stored.min = min(stored.b) stored.range = max(stored.b) - stored.min alter n. CA, vdw = (b - stored.min) / stored.range * 4 + 1 rebuild However, since the b-factor scales to the mean square displacement of the atom, you might also want to alter vdw radius like this: alter n. CA, vdw = (b / (8 * 3.14**2))**0.5 * 3 rebuild Cheers, Thomas Douglas Kojetin wrote, On 08/01/12 22:47: Hi Jason, Thanks -- is there any way to add some limits to the scaling, say to alter the vdw radius from a value of 1 to 5 based on a b-factor range of values? Doug On Jul 31, 2012, at 4:44 PM, Jason Vertrees wrote: Hi Douglas, You can do something as simple as this: # fetch a protein fetch 1ejg, async=0 # show as spheres as spheres, n. CA # set the vdw radii = some factor of the b-factor alter n. CA, vdw=b/5 rebuild Cheers, -- Jason On Tue, Jul 31, 2012 at 3:36 PM, Douglas Kojetin douglas.koje...@gmail.com wrote: Hi All, I would like to set the sphere size for each Ca atom proportional to the b-factor value (the larger the b-factor the larger the sphere size) and also color the sphere based on the b-factor value. Is there an easy way to adjust the sphere size according to b-factor value? Thanks, Doug -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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] weird distance measurements when pdb file contains symmetric atoms
Hi Pascal, the problem is that PyMOL looks up atoms by ID, which are not unique in your structure. Possible workarounds: 1) disable dynamic measures: PyMOL unset dynamic_measures 2) assign unique atom IDs: PyMOL stored.ID = 0 PyMOL alter all, ID=stored.ID=stored.ID+1 Cheers, Thomas Pascal Auffinger wrote, On 07/30/12 15:24: Hi, I encounter a weird behavior when I measure distances for atoms in the attached pdb files. The distances that are measured are not associated with the picked atoms but to some that have been generated by using the pymol symmetry options, with segi activated. Any ideas ? Thanks a lot, Pascal -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- 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
