Re: [PyMOL] Pymol Mobile viewer?
Hi, Sorry to dig up such an old thread, but now development time has been found for an iPad version of Pymol, can we hope for an Android version to appear at any point in the future? cheers, Doug > > Re: [PyMOL] Pymol Mobile viewer? > > Jason Vertrees Sun, 17 Jan 2010 06:48:31 -0800 > > Tsjerk, > > Warren and I discussed this months ago. While not really a great way > to spend development time, it would be fun to see PyMOL on one of the > mobile devices. In the meantime, check out Molecules > (http://www.sunsetlakesoftware.com/molecules) the only 3D molecular > viewer for mobile platforms that I'm aware of. > > > Thanks, > > -- J > > On Sun, Jan 17, 2010 at 5:20 AM, Tsjerk Wassenaar wrote: >> Hi Jason, >> >> Now what will come first? Pymol viewer for Android, for Mobile Windows >> or for iPhone? Would be so cool to show off at a conference, and use >> multi-touch to operate :p >> >> Cheers, >> >> Tsjerk >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> Computational Chemist >> Medicinal Chemist >> Neuropharmacologist >> >> -- >> Throughout its 18-year history, RSA Conference consistently attracts the >> world's best and brightest in the field, creating opportunities for >> Conference >> attendees to learn about information security's most important >> issues through >> interactions with peers, luminaries and emerging and established companies. >> http://p.sf.net/sfu/rsaconf-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 >> > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://p.sf.net/sfu/Zoho ___ 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 Mobile viewer?
Hi Thomas, Although I have no use for the iPad version I can answer your questions as if for an Android version. In my experience most people have quite a '2D' approach to molecular design, due to a lifetime of learning via lectures, journals and textbooks. Very often I find myself wishing I could show them a 3D representation of whatever it is we're talking about, without having to always lug my laptop around with me. So I would use it both for teaching and for aiding scientific discussion during project meetings, and also to aid in my thinking processes when I'm presented with dead time (e.g. on trains, planes etc.). I think under those circumstances some reduced functionality (esp. in the fanciness of graphics, moveiemaking etc.) wouldn't be a problem (although I'd want to keep all the Builder functions, including Sculpt and Clean). I would be willing to pay for it (in fact I would get the University to buy an Institute license so everyone, including students, could use it). cheers, Doug Quoting Thomas Holder on Mon, 13 Oct 2014 18:21:14 -0400: > Hi Doug, > > to answer your question, Schrödinger is not working on an Android > version of PyMOL and we don't have plans to start this any time soon. > > But we are happy to collect feedback that will help us prioritize an > Android port. For those who have an iPad: What do you use Mobile > PyMOL for? How often do you use it? Did you only install it because > it's for free or would you be willing to pay for it? Would you pay > for an Android version? Does the limited interface and reduced > functionality (compared to desktop PyMOL) satisfy your needs? If > not, which critical features are missing for you? > > Cheers, > Thomas > > On 11 Oct 2014, at 06:08, Douglas Houston wrote: > >> Hi, >> >> Sorry to dig up such an old thread, but now development time has been >> found for an iPad version of Pymol, can we hope for an Android version >> to appear at any point in the future? >> >> cheers, >> Doug >> >>> Re: [PyMOL] Pymol Mobile viewer? >>> >>> Jason Vertrees Sun, 17 Jan 2010 06:48:31 -0800 >>> >>> Tsjerk, >>> >>> Warren and I discussed this months ago. While not really a great way >>> to spend development time, it would be fun to see PyMOL on one of the >>> mobile devices. In the meantime, check out Molecules >>> (http://www.sunsetlakesoftware.com/molecules) the only 3D molecular >>> viewer for mobile platforms that I'm aware of. >>> >>> >>> Thanks, >>> >>> -- J >>> >>> On Sun, Jan 17, 2010 at 5:20 AM, Tsjerk Wassenaar >>> wrote: >>>> Hi Jason, >>>> >>>> Now what will come first? Pymol viewer for Android, for Mobile Windows >>>> or for iPhone? Would be so cool to show off at a conference, and use >>>> multi-touch to operate :p >>>> >>>> Cheers, >>>> >>>> Tsjerk >>>> >>>> -- >>>> Tsjerk A. Wassenaar, Ph.D. >>>> >>>> Computational Chemist >>>> Medicinal Chemist >>>> Neuropharmacologist > > -- > Thomas Holder > PyMOL Developer > Schrödinger, Inc. > > > _ Dr. Douglas R. Houston Lecturer Institute of Structural and Molecular Biology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 http://tinyurl.com/douglasrhouston -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ 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] Access API without the GUI
Hi all, Does anyone know if there's a way of accessing Pymol's API without the GUI? There are some useful functions in there and my loops would iterate a lot faster if the GUI didn't fire up every time. cheers, Doug _ Dr. Douglas R. Houston Lecturer Institute of Structural and Molecular Biology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 http://tinyurl.com/douglasrhouston -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Access API without the GUI
Thanks everyone, that works a treat.
Quoting Matthew Baumgartner on Tue, 11 Nov 2014
15:10:38 -0500:
> Hi Doug,
> Check out these pages on integrating PyMOL into a python script.
> Essentially you will write a python script that imports pymol. From
> there you can do things like load objects, align them, or anything
> else.
>
> http://www.pymolwiki.org/index.php/Python_Integration
> http://www.pymolwiki.org/index.php/Launching_From_a_Script
>
> The key part is that you pass the parameters '-qc' to pymol. 'q' is
> for quiet, to supress some of Pymol's output, and 'c' is for command
> line versions, i.e. don't launch the GUI.
>
>
> import __main__
> __main__.pymol_argv = [ 'pymol', '-*qc*' ]
>
> # Importing the PyMOL module will create the window.
> import pymol
>
> # Call the function below before using any PyMOL modules.
> pymol.finish_launching()
>
> from pymol import cmd
>
> #now your commands
> cmd.fetch('1YCR')
>
> #
>
>
> You may also want to check out these pages on scripting:
>
> http://www.pymolwiki.org/index.php/Simple_Scripting
> http://www.pymolwiki.org/index.php/Advanced_Scripting
>
>
> On 11/11/2014 02:56 PM, Douglas Houston wrote:
>> Hi all,
>>
>> Does anyone know if there's a way of accessing Pymol's API without the
>> GUI? There are some useful functions in there and my loops would
>> iterate a lot faster if the GUI didn't fire up every time.
>>
>> cheers,
>> Doug
>> _
>> Dr. Douglas R. Houston
>> Lecturer
>> Institute of Structural and Molecular Biology
>> Room 3.23, Michael Swann Building
>> King's Buildings
>> University of Edinburgh
>> Edinburgh, EH9 3JR, UK
>> Tel. 0131 650 7358
>> http://tinyurl.com/douglasrhouston
>>
>
>
_
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
--
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[PyMOL] Optimize plugin throws "NameError: global name 'ob' is not defined"
Hi all, I installed Optimize.py, now when I start Pymol I see: "Optimize plug-in needs openbabel to be installed in your system, please follow the instructions at http://openbabel.org/wiki/Get_Open_Babel"; If I try to use any optimize commands I get: "PyMOL>minimize all, nsteps 2 Traceback (most recent call last): File "/usr/people/douglas/programs/pymol-v1.7.2.3/modules/pymol/parser.py", line 254, in parse self.result=apply(layer.kw[0],layer.args,layer.kw_args) File "/usr/people/douglas/programs/pymol-v1.7.2.3/modules/pmg_tk/startup/optimize.py", line 237, in minimize obconversion = ob.OBConversion() NameError: global name 'ob' is not defined " Open Babel IS installed on my system (v2.3.2), do I need to tell Pymol where? cheers, Doug -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Optimize plugin throws "NameError: global name 'ob' is not defined"
Thanks Matt, that is indeed the problem: Python 2.5.1 (r251:54863, Sep 21 2007, 11:20:07) [GCC 3.2.3 20030502 (Red Hat Linux 3.2.3-56)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import openbabel Traceback (most recent call last): File "", line 1, in ImportError: No module named openbabel I have tried recompiling Open Babel with the Python bindings but it fails with (and I realise this is no longer a Pymol problem so I will get on to the Open Babel mailing list): [100%] Building CXX object scripts/CMakeFiles/bindings_python.dir/python/openbabel-python.cpp.o Linking CXX executable ../bin/test_unitcell [100%] Built target test_unitcell Linking CXX shared module ../lib/_openbabel.so /usr/local/lib/libpython2.7.a(thread.o): In function `_pythread_pthread_set_stacksize': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:497: undefined reference to `pthread_attr_setstacksize' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_release_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_free_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:294: undefined reference to `sem_destroy' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined reference to `sem_init' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_acquire_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:326: undefined reference to `sem_trywait' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:324: undefined reference to `sem_wait' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_start_new_thread': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:184: undefined reference to `pthread_attr_setstacksize' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:194: undefined reference to `pthread_create' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:210: undefined reference to `pthread_detach' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_release_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:350: undefined reference to `sem_post' /usr/local/lib/libpython2.7.a(thread.o): In function `PyThread_allocate_lock': /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined reference to `sem_init' /usr/bin/tmp/Python-2.7.6/Python/thread_pthread.h:269: undefined reference to `sem_init' /usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_forkpty': /usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3958: undefined reference to `forkpty' /usr/local/lib/libpython2.7.a(posixmodule.o): In function `posix_openpty': /usr/bin/tmp/Python-2.7.6/./Modules/posixmodule.c:3898: undefined reference to `openpty' collect2: ld returned 1 exit status make[2]: *** [lib/_openbabel.so] Error 1 make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2 make: *** [all] Error 2 Quoting Matthew Baumgartner on Wed, 12 Nov 2014 08:55:27 -0500: > Hi, > Can you check to see if the python bindings are compiled openbabel? > > On the bash command line, run the command 'python' to get an interactive > shell and then run 'import openbabel'. > > Matt > > On 11/12/2014 07:14 AM, Douglas Houston wrote: >> Hi all, >> >> I installed Optimize.py, now when I start Pymol I see: >> >> "Optimize plug-in needs openbabel to be installed in your system, >> please follow the instructions at >> http://openbabel.org/wiki/Get_Open_Babel"; >> >> If I try to use any optimize commands I get: >> >> "PyMOL>minimize all, nsteps 2 >> Traceback (most recent call last): >> File >> "/usr/people/douglas/programs/pymol-v1.7.2.3/modules/pymol/parser.py", >> line 254, in parse >> self.result=apply(layer.kw[0],layer.args,layer.kw_args) >> File >> "/usr/people/douglas/programs/pymol-v1.7.2.3/modules/pmg_tk/startup/optimize.py", >> line 237, >> in >> minimize >> obconversion = ob.OBConversion() >> NameError: global name 'ob' is not defined >> " >> >> Open Babel IS installed on my system (v2.3.2), do I need to tell >> Pymol where? >> >> cheers, >> Doug >> >> > > > -- > Compr
Re: [PyMOL] Access API without the GUI
Surely there must be a way to run Pymol in a mode that does not fire up the GUI but still allows it access to OpenGL?? > Michael, > > The "-c" option forces PyMOL to run in command-line-only mode which means it > doesn't have access to the OpenGL hardware (used by cmd.draw and interactive > graphics). In command-line-only mode, ray tracing (cmd.ray) is the only > option. > > Cheers, > Warren > >> -Original Message- >> From: pymol-users-bounces@... [mailto:pymol-users-bounces@...] On >> Behalf Of Michael Lerner >> Sent: Thursday, October 25, 2007 8:31 AM >> To: pymol mailinglist >> Subject: [PyMOL] Trouble making pictures in a script >> >> Hi, >> >> I have a Python script that sets a system up and then calls >> cmd.png() to render an image. I use it to process several files at >> a time, and there's no need to look at it while it's working, so I >> use >> >> pymol -qcr myscript.py >> >> to launch it. It works fine when I ray trace things, but if I just >> set the system up and call cmd.png(), I get this error: >> >> ScenePNG-WARNING: invalid context or no image. >> >> Calling cmd.draw() instead of cmd.ray() doesn't seem to fix things. >> Any ideas? Some of the systems are big enough that cmd.ray() fails, >> so I'd like to be able to find a workaround. >> >> Thanks, >> >> -michael >> >> -- >> Biophysics Graduate Student >> Carlson Lab, University of Michigan >> http://www.umich.edu/~mlerner >> >> -- >> --- >> This SF.net email is sponsored by: Splunk Inc. >> Still grepping through log files to find problems? Stop. >> Now Search log events and configuration files using AJAX and a browser. >> Download your FREE copy of Splunk now >> http://get.splunk.com/ >> ___ >> PyMOL-users mailing list >> PyMOL-users@... >> https://lists.sourceforge.net/lists/listinfo/pymol-users > > > _ > Dr. Douglas R. Houston > Lecturer > Institute of Structural and Molecular Biology > Room 3.23, Michael Swann Building > King's Buildings > University of Edinburgh > Edinburgh, EH9 3JR, UK > Tel. 0131 650 7358 > http://tinyurl.com/douglasrhouston > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] best way to rotate molecular bonds without dihedral context?
Hi John, Does the 'torsion' command work? Cheers, Doug Quoting johnbax...@cs.unm.edu on Thu, 20 Nov 2014 01:06:04 -0700: > Hello, PyMOL users! > > I am trying to figure out within the Python interface how to rotate the > parts of a molecule on one side of a bond about that bond's axis, given > only the two atoms defining the bond and a angle to rotate by (that is, > without requiring me to specify four atoms and a final dihedral angle > value as required by set_dihedral). While I understand the "rotate" > function, I can't figure out how, in the Python interface, to select the > atoms on one side of a bond given the bond's two defining atoms. > > I've looked through the PyMOL C++ code, and it appears that this > functionality is provided by the layer3/Selector.cpp function > "SelectorSubdivide" when its "bondMode" flag set to true and given two > atoms; set_dihedral's C++ implementation seems to use this functionality > to select the atoms it will rotate. I tried to look through the rest of > the source to see if this selection behavior was somehow exposed to the > Python interface, but as best as I could tell it doesn't seem to be. > > If anyone can work out a good way from the Python interface to select the > atoms of a molecule on one side of a bond, or if there is a > Python-accessible function that acts similar to set_dihedral but rotates > about any bond by a given angular change without requiring a bonded > sequence of four atoms to define an arbitrary dihedral plane (and an > otherwise unnecessary call to get_dihedral to to calculate the change > needed to know what angle I would need to give set_dihedral), I would be > very appreciative. > > Thank you very much for your time! > > -John > > > -- > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > _ Dr. Douglas R. Houston Lecturer Institute of Structural and Molecular Biology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 http://tinyurl.com/douglasrhouston -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] best way to rotate molecular bonds without dihedral context?
That's alright, I only discovered the "Volume" feature yesterday and that's been around since v1.4 ... Quoting johnbax...@cs.unm.edu on Thu, 20 Nov 2014 11:06:39 -0700: > It does! Thank you very much; I don't know how I missed that command. > >> Hi John, >> >> Does the 'torsion' command work? >> >> Cheers, >> Doug >> >> >> Quoting johnbax...@cs.unm.edu on Thu, 20 Nov 2014 01:06:04 -0700: >> >>> Hello, PyMOL users! >>> >>> I am trying to figure out within the Python interface how to rotate the >>> parts of a molecule on one side of a bond about that bond's axis, given >>> only the two atoms defining the bond and a angle to rotate by (that is, >>> without requiring me to specify four atoms and a final dihedral angle >>> value as required by set_dihedral). While I understand the "rotate" >>> function, I can't figure out how, in the Python interface, to select the >>> atoms on one side of a bond given the bond's two defining atoms. >>> >>> I've looked through the PyMOL C++ code, and it appears that this >>> functionality is provided by the layer3/Selector.cpp function >>> "SelectorSubdivide" when its "bondMode" flag set to true and given two >>> atoms; set_dihedral's C++ implementation seems to use this functionality >>> to select the atoms it will rotate. I tried to look through the rest of >>> the source to see if this selection behavior was somehow exposed to the >>> Python interface, but as best as I could tell it doesn't seem to be. >>> >>> If anyone can work out a good way from the Python interface to select >>> the >>> atoms of a molecule on one side of a bond, or if there is a >>> Python-accessible function that acts similar to set_dihedral but rotates >>> about any bond by a given angular change without requiring a bonded >>> sequence of four atoms to define an arbitrary dihedral plane (and an >>> otherwise unnecessary call to get_dihedral to to calculate the change >>> needed to know what angle I would need to give set_dihedral), I would be >>> very appreciative. >>> >>> Thank you very much for your time! >>> >>> -John >>> >>> >>> -- >>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >>> with Interactivity, Sharing, Native Excel Exports, App Integration & >>> more >>> Get technology previously reserved for billion-dollar corporations, FREE >>> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk >>> ___ >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >>> >>> >> >> >> >> >> _ >> Dr. Douglas R. Houston >> Lecturer >> Institute of Structural and Molecular Biology >> Room 3.23, Michael Swann Building >> King's Buildings >> University of Edinburgh >> Edinburgh, EH9 3JR, UK >> Tel. 0131 650 7358 >> http://tinyurl.com/douglasrhouston >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336. >> >> >> >> -- >> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server >> from Actuate! Instantly Supercharge Your Business Reports and Dashboards >> with Interactivity, Sharing, Native Excel Exports, App Integration & more >> Get technology previously reserved for billion-dollar corporations, FREE >> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > > > > -- > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, FREE > http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > _ Dr. Douglas R. Houston Lecturer Institute of Structural and Molecular Biology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 http://tinyurl.com/dougl
Re: [PyMOL] Detecting holes/cavities in surface
Hi Daniel, If you don't HAVE to use Pymol, something like fPocket, HOLE or PocketDepth from this list might do what you want: http://www.vls3d.com/links/bioinformatics/binding-pockets You might find this list interesting too: http://www.vls3d.com/links/bioinformatics/peptides-antibodies-epitopes cheers, Doug Quoting Andreas Warnecke <4ndreas.warne...@gmail.com> on Wed, 20 Jul 2016 00:57:39 +0200: > I haven't used it before, but I there is a PyMOL plugin called KVfinder > that detects cavities. Potentially this offers an approach for you. > On Jul 20, 2016 12:05 AM, "Daniel James" wrote: > >> Hi all, >> >> I haven't used this list before but can't find an answer to my question >> elsewhere. I am selecting the antibody binding site automatically to >> calculate the surface area of the binding sites. >> >> However, some of the binding sites have holes/cavities in the surface - I >> would like to be able to detect if a surface has a hole in it on PyMol (to >> make a note that it needs to be looked at manually). >> >> I create an object of the antigen binding site, show surface and then use >> get_area to get SASA. >> >> Any help will be appreciated. >> >> Thanks, >> Daniel >> >> >> -- >> What NetFlow Analyzer can do for you? Monitors network bandwidth and >> traffic >> patterns at an interface-level. Reveals which users, apps, and protocols >> are >> consuming the most bandwidth. Provides multi-vendor support for NetFlow, >> J-Flow, sFlow and other flows. Make informed decisions using capacity >> planning >> reports.http://sdm.link/zohodev2dev >> ___ >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> > _ Dr. Douglas R. Houston Senior Lecturer in Computational Biochemistry Institute of Quantitative Biology, Biochemistry and Biotechnology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev ___ 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
