Hello, I have gone through the tutorial and follow every single step. The plugin said it successfully generate the receptor pdbqt file. However, when I get to the docking, it still cannot detect the receptor so I cannot run any autogrid or autodock. Is there any reason for that?
Thank you very much! Sing On Feb 19, 2010, at 11:41 AM, Shiven Shandilya wrote: > Hello Sing, > > Perhaps going over the basic tutorial will help make things clear: > > http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html > > > Best, > Shiven > > > > On Fri, Feb 19, 2010 at 1:13 PM, Kin Sing Stephen Lee > <s...@chemistry.msu.edu> wrote: >> Dear all, >> >> Sorry I fixed the prepare_ligand4.py problem. However, when I try to >> do the autodock in the plugin, the plugin cannot recognize the >> receptor so there is no choice available in the receptor in the >> docking page. If I click autogrid or autodock, the program shows no >> response. Is there any setting I could check and fix it? >> >> Thank you very much >> >> Sing >> >> On Feb 19, 2010, at 9:33 AM, pymol-users- >> requ...@lists.sourceforge.net >> wrote: >> >>> Send PyMOL-users mailing list submissions to >>> pymol-users@lists.sourceforge.net >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>> or, via email, send a message with subject or body 'help' to >>> pymol-users-requ...@lists.sourceforge.net >>> >>> You can reach the person managing the list at >>> pymol-users-ow...@lists.sourceforge.net >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of PyMOL-users digest..." >>> >>> >>> Today's Topics: >>> >>> 1. Re: coordinate systems of pymol and povray (Tsjerk Wassenaar) >>> 2. FreeMOL (Jason Vertrees) >>> 3. Re: PyMOL-users Digest, Vol 45, Issue 9 (Kin Sing Stephen Lee) >>> 4. Save movie not working (Kent Rossman) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Thu, 18 Feb 2010 21:42:39 +0100 >>> From: Tsjerk Wassenaar <tsje...@gmail.com> >>> Subject: Re: [PyMOL] coordinate systems of pymol and povray >>> To: gabriela.schlau-co...@alumni.brown.edu, pymol-users >>> <pymol-users@lists.sourceforge.net> >>> Message-ID: >>> <8ff898151002181242o50721274q14324f2a14209...@mail.gmail.com> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> Hi Gabriela, >>> >>> If you only want to get the molecule back in view and rotate/ >>> translate >>> it to your liking, you can use commands like: >>> >>> #declare Protein = union { #include "protein.inc" } >>> #declare Center = (min_extent(Protein)+max_extent(Protein))/2; >>> object { Protein translate -Center } >>> >>> If you want to preserve the view you had in Pymol, you'll need >>> something more. For this purpose I wrote a set of POV-Ray macros, >>> which are attached. For this to work, you have to save the view from >>> get_view(). If you used the (better ;)) second version of make_pov >>> from the wiki, the view is already saved in the pov-ray file. Place >>> the macro file somewhere where POV-Ray can find it, and uncomment >>> the >>> section in the .pov file starting with "Uncomment the following >>> lines" :) Now, if you want to add objects to your scene that you >>> have >>> defined based on the coordinates in the pdb file, you can use >>> something like: >>> >>> // This draws a sphere of radius 1 at the origin of your .pdb >>> coordinate system >>> sphere { 0, 1 SET_PYMOL_VIEW( PYMOL_VIEW )) } >>> >>> For more extensive information, read the first section of the >>> file. If >>> things are still unclear, feel free to contact me. And if you find >>> that you've managed to do really cool stuff with it, please let me >>> know :) >>> >>> >>> Hope it helps, >>> >>> Tsjerk >>> >>> On Wed, Feb 17, 2010 at 5:07 PM, Gabriela Schlau-Cohen >>> <gsad...@hotmail.com> wrote: >>>> Hi all, >>>> >>>> I am trying to load a pymol graphic into povray and then add on >>>> geometric >>>> objects.? I exported and loaded the molecular model from pymol >>>> successfully >>>> using the make_pov.py script from the wiki. ?I can then copy and >>>> paste that >>>> file into povray to generate the molecules through povray. ?Then, >>>> when I >>>> save the object in pymol to get the molecular coordinates, the >>>> coordinates >>>> are in a different system. >>>> Can someone tell me how to get the molecular coordinates and a >>>> povray file >>>> in the same coordinate system? >>>> Thanks, >>>> Gabriela >>>> ________________________________ >>>> Hotmail: Trusted email with powerful SPAM protection. Sign up now. >>>> ------------------------------------------------------------------------------ >>>> Download Intel? Parallel Studio Eval >>>> Try the new software tools for yourself. Speed compiling, find bugs >>>> proactively, and fine-tune applications for parallel performance. >>>> See why Intel Parallel Studio got high marks during beta. >>>> http://p.sf.net/sfu/intel-sw-dev >>>> _______________________________________________ >>>> 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 >>>> >>> >>> >>> >>> -- >>> Tsjerk A. Wassenaar, Ph.D. >>> >>> Computational Chemist >>> Medicinal Chemist >>> Neuropharmacologist >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: pymolmacro.inc.gz >>> Type: application/x-gzip >>> Size: 2390 bytes >>> Desc: not available >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Thu, 18 Feb 2010 16:36:40 -0500 >>> From: Jason Vertrees <jason.vertr...@schrodinger.com> >>> Subject: [PyMOL] FreeMOL >>> To: pymol-users@lists.sourceforge.net >>> Message-ID: >>> <79558d781002181336x4216e157w7181f92f24cbd...@mail.gmail.com> >>> Content-Type: text/plain; charset=ISO-8859-1 >>> >>> PyMOLers, >>> >>> The FreeMOL website is back up as it was before (http:// >>> freemol.org). >>> FreeMOL is still open-source, based off the original bioinformatics >>> project. The only difference is the location of the webserver: it >>> is >>> now running from a Schrodinger server to give me better access >>> (again, >>> Warren's servers only had FTP access, we now have ssh). >>> >>> Please let me know if anything's missing. >>> >>> Thanks for being patient, >>> >>> -- Jason >>> >>> -- >>> Jason Vertrees, PhD >>> PyMOL Product Manager >>> Schrodinger, LLC >>> >>> (e) jason.vertr...@schrodinger.com >>> (o) +1 (603) 374-7120 >>> >>> >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Fri, 19 Feb 2010 01:37:24 -0800 >>> From: Kin Sing Stephen Lee <leek...@msu.edu> >>> Subject: Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 9 >>> To: pymol-users@lists.sourceforge.net >>> Message-ID: <23b94f8e-04b7-4718-8758-90b247c5d...@msu.edu> >>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >>> >>> Thank you Daniel, >>> >>> I finally found the Autodock tool path in Mac however, i got another >>> error message: "ImportError: No module named MolKit" Is there any >>> solution for this in Mac? >>> >>> Thank you very much >>> >>> Sing >>> >>> On Feb 18, 2010, at 10:56 AM, pymol-users- >>> requ...@lists.sourceforge.net wrote: >>> >>>> Send PyMOL-users mailing list submissions to >>>> pymol-users@lists.sourceforge.net >>>> >>>> To subscribe or unsubscribe via the World Wide Web, visit >>>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> or, via email, send a message with subject or body 'help' to >>>> pymol-users-requ...@lists.sourceforge.net >>>> >>>> You can reach the person managing the list at >>>> pymol-users-ow...@lists.sourceforge.net >>>> >>>> When replying, please edit your Subject line so it is more specific >>>> than "Re: Contents of PyMOL-users digest..." >>>> >>>> >>>> Today's Topics: >>>> >>>> 1. Autodock plugin (Kin Sing Stephen Lee) >>>> 2. Re: Autodock plugin (Daniel Seeliger) >>>> 3. Update & Submitting Bugs (Jason Vertrees) >>>> 4. Re: Update & Submitting Bugs (Christoph Gohlke) >>>> 5. Re: Update & Submitting Bugs (Jason Vertrees) >>>> 6. Re: Update & Submitting Bugs (Christoph Gohlke) >>>> 7. Regarding the Control panel in pymol (phani ghanakota) >>>> 8. Re: Regarding the Control panel in pymol (Jason Vertrees) >>>> 9. coordinate systems of pymol and povray (Gabriela Schlau-Cohen) >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Tue, 16 Feb 2010 11:06:40 -0800 >>>> From: Kin Sing Stephen Lee <leek...@msu.edu> >>>> Subject: [PyMOL] Autodock plugin >>>> To: "pymol-users@lists.sourceforge.net" >>>> <pymol-users@lists.sourceforge.net> >>>> Message-ID: <333eebd7-7c78-48d5-90ae-ff9907837...@msu.edu> >>>> Content-Type: text/plain; charset=US-ASCII; format=flowed; >>>> delsp=yes >>>> >>>> Dear all, >>>> >>>> This is the first time for me to use the autodock plugin and I have >>>> some simple questions. I'm using Macbook Pro (OS X v 10.5 - >>>> leopard). Autodock and autodock tools run fine in the X11 >>>> terminal. >>>> In the autodock plugin, I need to put in the autodock tool program >>>> path,so I put in the path where I installed the autodock tool >>>> (under >>>> applications folder). When I tried to prepare my receptor and >>>> ligand >>>> file, the plugin cannot find the autodock tools >>>> (prepare_receptor4.py >>>> as well as prepare_ligand4.py) so I am wondering where I can find >>>> the >>>> autodock tools program path or is it possible to use the plugin in >>>> mac? >>>> >>>> Thank you very much >>>> >>>> Sing >>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 2 >>>> Date: Tue, 16 Feb 2010 20:26:00 +0100 >>>> From: Daniel Seeliger <dsee...@gwdg.de> >>>> Subject: Re: [PyMOL] Autodock plugin >>>> To: pymol-users@lists.sourceforge.net >>>> Message-ID: <201002162026.00620.dsee...@gwdg.de> >>>> Content-Type: Text/Plain; charset="iso-8859-1" >>>> >>>> Hi Sing, >>>> >>>> take a look into >>>> ~/.ADplugin/pymol_autodock_plugin.conf >>>> and set the path to the autodocktools scripts correctly. Then the >>>> plugin >>>> should find them. >>>> >>>> Cheers, >>>> Daniel >>>> >>>> On Tuesday 16 February 2010 08:06:40 pm Kin Sing Stephen Lee wrote: >>>>> Dear all, >>>>> >>>>> This is the first time for me to use the autodock plugin and I >>>>> have >>>>> some simple questions. I'm using Macbook Pro (OS X v 10.5 - >>>>> leopard). Autodock and autodock tools run fine in the X11 >>>>> terminal. >>>>> In the autodock plugin, I need to put in the autodock tool program >>>>> path,so I put in the path where I installed the autodock tool >>>>> (under >>>>> applications folder). When I tried to prepare my receptor and >>>>> ligand >>>>> file, the plugin cannot find the autodock tools >>>>> (prepare_receptor4.py >>>>> as well as prepare_ligand4.py) so I am wondering where I can find >>>>> the >>>>> autodock tools program path or is it possible to use the plugin in >>>>> mac? >>>>> >>>>> Thank you very much >>>>> >>>>> Sing >>>>> >>>>> >>>>> --------------------------------------------------------------------------- >>>>> --- SOLARIS 10 is the OS for Data Centers - provides features such >>>>> as >>>>> DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris >>>>> 10 NOW >>>>> http://p.sf.net/sfu/solaris-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 >>>>> >>>> >>>> -- >>>> Dr. Daniel Seeliger >>>> Computational Biomolecular Dynamics Group >>>> Max-Planck-Institute for Biophysical Chemistry >>>> Tel. +49 (0) 551-201-2310 >>>> http://wwwuser.gwdg.de/~dseelig >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 3 >>>> Date: Wed, 17 Feb 2010 14:35:13 -0500 >>>> From: Jason Vertrees <jason.vertr...@schrodinger.com> >>>> Subject: [PyMOL] Update & Submitting Bugs >>>> To: pymol-users@lists.sourceforge.net >>>> Message-ID: >>>> <79558d781002171135l2f74c6cax60c357bc8e4b...@mail.gmail.com> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> PyMOLers, >>>> >>>> * In order to keep all bugs in one place please email your bugs to >>>> h...@schrodinger.com instead of using the SourceForge tracker. >>>> Schrodinger has a very nice bug tracker that we use; and, in the >>>> end >>>> it's just better to not duplicate effort. >>>> >>>> * I started pushing small changes into the open-source code and >>>> more >>>> are coming. Please file bugs to the aforementioned address. >>>> >>>> * CEAlign is working on all my versions of PyMOL, so I'll be >>>> pushing >>>> that to the open-source soon. >>>> >>>> * We now have another server for FreeMOL (which maps right back to >>>> http://freemol.org/) and we also have control over the FreeMOL >>>> project. When I get back to my office (where the files live) I'll >>>> update FreeMOL. >>>> >>>> Thanks, >>>> >>>> -- Jason >>>> >>>> -- >>>> Jason Vertrees, PhD >>>> PyMOL Product Manager >>>> Schrodinger, LLC >>>> >>>> (e) jason.vertr...@schrodinger.com >>>> (o) +1 (603) 374-7120 >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 4 >>>> Date: Wed, 17 Feb 2010 21:15:06 -0800 >>>> From: Christoph Gohlke <cgoh...@uci.edu> >>>> Subject: Re: [PyMOL] Update & Submitting Bugs >>>> To: pymol-users@lists.sourceforge.net >>>> Message-ID: <4b7cccda.90...@uci.edu> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> What is the URL of the Schrodinger bug tracker? The PyMOL >>>> SourceForge >>>> tracker is disabled. >>>> >>>> Thanks, >>>> >>>> Christoph >>>> >>>> >>>> On 2/17/2010 11:35 AM, Jason Vertrees wrote: >>>>> PyMOLers, >>>>> >>>>> * In order to keep all bugs in one place please email your bugs to >>>>> h...@schrodinger.com instead of using the SourceForge tracker. >>>>> Schrodinger has a very nice bug tracker that we use; and, in the >>>>> end >>>>> it's just better to not duplicate effort. >>>>> >>>>> * I started pushing small changes into the open-source code and >>>>> more >>>>> are coming. Please file bugs to the aforementioned address. >>>>> >>>>> * CEAlign is working on all my versions of PyMOL, so I'll be >>>>> pushing >>>>> that to the open-source soon. >>>>> >>>>> * We now have another server for FreeMOL (which maps right back to >>>>> http://freemol.org/) and we also have control over the FreeMOL >>>>> project. When I get back to my office (where the files live) I'll >>>>> update FreeMOL. >>>>> >>>>> Thanks, >>>>> >>>>> -- Jason >>>>> >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 5 >>>> Date: Thu, 18 Feb 2010 00:30:49 -0500 >>>> From: Jason Vertrees <jason.vertr...@schrodinger.com> >>>> Subject: Re: [PyMOL] Update & Submitting Bugs >>>> To: Christoph Gohlke <cgoh...@uci.edu> >>>> Cc: pymol-users@lists.sourceforge.net >>>> Message-ID: >>>> <79558d781002172130y46763880j59563bd7a908c...@mail.gmail.com> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> Christoph, >>>> >>>> Schrodinger's tracker is internal only. To submit a bug, just >>>> email >>>> your bugs to h...@schrodinger.com (for faster turnaround put >>>> something >>>> like "PyMOL Bug" in the title). They are immediately filed and >>>> assigned to me. >>>> >>>> I chose to turn off the SourceForge tracker because I do not want >>>> to >>>> miss bugs or spend my time duplicating tracking efforts, as I was. >>>> >>>> Thanks, >>>> >>>> -- Jason >>>> >>>> On Thu, Feb 18, 2010 at 12:15 AM, Christoph Gohlke >>>> <cgoh...@uci.edu> >>>> wrote: >>>>> What is the URL of the Schrodinger bug tracker? The PyMOL >>>>> SourceForge >>>>> tracker is disabled. >>>>> >>>>> Thanks, >>>>> >>>>> Christoph >>>>> >>>>> >>>>> On 2/17/2010 11:35 AM, Jason Vertrees wrote: >>>>>> PyMOLers, >>>>>> >>>>>> * In order to keep all bugs in one place please email your bugs >>>>>> to >>>>>> h...@schrodinger.com instead of using the SourceForge tracker. >>>>>> Schrodinger has a very nice bug tracker that we use; and, in the >>>>>> end >>>>>> it's just better to not duplicate effort. >>>>>> >>>>>> * I started pushing small changes into the open-source code and >>>>>> more >>>>>> are coming. ?Please file bugs to the aforementioned address. >>>>>> >>>>>> * CEAlign is working on all my versions of PyMOL, so I'll be >>>>>> pushing >>>>>> that to the open-source soon. >>>>>> >>>>>> * We now have another server for FreeMOL (which maps right back >>>>>> to >>>>>> http://freemol.org/) and we also have control over the FreeMOL >>>>>> project. ?When I get back to my office (where the files live) >>>>>> I'll >>>>>> update FreeMOL. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> -- Jason >>>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Download Intel® Parallel Studio Eval >>>>> Try the new software tools for yourself. Speed compiling, find >>>>> bugs >>>>> proactively, and fine-tune applications for parallel performance. >>>>> See why Intel Parallel Studio got high marks during beta. >>>>> http://p.sf.net/sfu/intel-sw-dev >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 6 >>>> Date: Wed, 17 Feb 2010 23:23:26 -0800 >>>> From: Christoph Gohlke <cgoh...@uci.edu> >>>> Subject: Re: [PyMOL] Update & Submitting Bugs >>>> To: Jason Vertrees <jason.vertr...@schrodinger.com> >>>> Cc: pymol-users@lists.sourceforge.net >>>> Message-ID: <4b7ceaee.4000...@uci.edu> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> Good. Thanks for keeping PyMOL development going. >>>> >>>> Christoph >>>> >>>> On 2/17/2010 9:30 PM, Jason Vertrees wrote: >>>>> Christoph, >>>>> >>>>> Schrodinger's tracker is internal only. To submit a bug, just >>>>> email >>>>> your bugs to h...@schrodinger.com (for faster turnaround put >>>>> something >>>>> like "PyMOL Bug" in the title). They are immediately filed and >>>>> assigned to me. >>>>> >>>>> I chose to turn off the SourceForge tracker because I do not >>>>> want to >>>>> miss bugs or spend my time duplicating tracking efforts, as I was. >>>>> >>>>> Thanks, >>>>> >>>>> -- Jason >>>>> >>>>> On Thu, Feb 18, 2010 at 12:15 AM, Christoph Gohlke >>>>> <cgoh...@uci.edu> wrote: >>>>>> What is the URL of the Schrodinger bug tracker? The PyMOL >>>>>> SourceForge >>>>>> tracker is disabled. >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Christoph >>>>>> >>>>>> >>>>>> On 2/17/2010 11:35 AM, Jason Vertrees wrote: >>>>>>> PyMOLers, >>>>>>> >>>>>>> * In order to keep all bugs in one place please email your >>>>>>> bugs to >>>>>>> h...@schrodinger.com instead of using the SourceForge tracker. >>>>>>> Schrodinger has a very nice bug tracker that we use; and, in the >>>>>>> end >>>>>>> it's just better to not duplicate effort. >>>>>>> >>>>>>> * I started pushing small changes into the open-source code and >>>>>>> more >>>>>>> are coming. Please file bugs to the aforementioned address. >>>>>>> >>>>>>> * CEAlign is working on all my versions of PyMOL, so I'll be >>>>>>> pushing >>>>>>> that to the open-source soon. >>>>>>> >>>>>>> * We now have another server for FreeMOL (which maps right >>>>>>> back to >>>>>>> http://freemol.org/) and we also have control over the FreeMOL >>>>>>> project. When I get back to my office (where the files live) >>>>>>> I'll >>>>>>> update FreeMOL. >>>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> -- Jason >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 7 >>>> Date: Thu, 18 Feb 2010 09:30:34 -0800 (PST) >>>> From: phani ghanakota <gphanionl...@yahoo.com> >>>> Subject: [PyMOL] Regarding the Control panel in pymol >>>> To: pymol-users@lists.sourceforge.net >>>> Message-ID: <820965.90400...@web110014.mail.gq1.yahoo.com> >>>> Content-Type: text/plain; charset="us-ascii" >>>> >>>> Hi, >>>> >>>> Is there a way to toggle on and off the control panel using a >>>> command. So that viewing in the full screen mode would be more >>>> pleasant. >>>> >>>> Thanks in advance. >>>> >>>> >>>> >>>> >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> >>>> ------------------------------ >>>> >>>> Message: 8 >>>> Date: Thu, 18 Feb 2010 13:54:40 -0500 >>>> From: Jason Vertrees <jason.vertr...@schrodinger.com> >>>> Subject: Re: [PyMOL] Regarding the Control panel in pymol >>>> To: phani ghanakota <gphanionl...@yahoo.com> >>>> Cc: pymol-users@lists.sourceforge.net >>>> Message-ID: >>>> <79558d781002181054o70d34b6h803e7d385c88e...@mail.gmail.com> >>>> Content-Type: text/plain; charset=ISO-8859-1 >>>> >>>> On Thu, Feb 18, 2010 at 12:30 PM, phani ghanakota >>>> <gphanionl...@yahoo.com> wrote: >>>>> Is there a way to toggle on and off the control panel using a >>>>> command. So that viewing in the full screen mode would be more >>>>> pleasant. >>>> >>>> Phani, >>>> >>>> # turns off the internal UI >>>> set internal_gui, 0 >>>> >>>> # make PyMOL fullscreen; works on Windows and Mac; some issues on >>>> Linux >>>> fullscreen >>>> >>>> -- Jason >>>> >>>> -- >>>> Jason Vertrees, PhD >>>> PyMOL Product Manager >>>> Schrodinger, LLC >>>> >>>> (e) jason.vertr...@schrodinger.com >>>> (o) +1 (603) 374-7120 >>>> >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 9 >>>> Date: Wed, 17 Feb 2010 16:07:05 +0000 >>>> From: Gabriela Schlau-Cohen <gsad...@hotmail.com> >>>> Subject: [PyMOL] coordinate systems of pymol and povray >>>> To: <pymol-users@lists.sourceforge.net> >>>> Message-ID: <snt109-w258456a7a08f0be0bf5c52a4...@phx.gbl> >>>> Content-Type: text/plain; charset="iso-8859-1" >>>> >>>> >>>> Hi all, >>>> >>>> I am trying to load a pymol graphic into povray and then add on >>>> geometric objects. I exported and loaded the molecular model from >>>> pymol successfully using the make_pov.py script from the wiki. I >>>> can then copy and paste that file into povray to generate the >>>> molecules through povray. Then, when I save the object in pymol to >>>> get the molecular coordinates, the coordinates are in a different >>>> system. >>>> Can someone tell me how to get the molecular coordinates and a >>>> povray file in the same coordinate system? >>>> Thanks,Gabriela >>>> _________________________________________________________________ >>>> Hotmail: Trusted email with powerful SPAM protection. >>>> http://clk.atdmt.com/GBL/go/201469227/direct/01/ >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> >>>> ------------------------------ >>>> >>>> ------------------------------------------------------------------------------ >>>> Download Intel® Parallel Studio Eval >>>> Try the new software tools for yourself. Speed compiling, find bugs >>>> proactively, and fine-tune applications for parallel performance. >>>> See why Intel Parallel Studio got high marks during beta. >>>> http://p.sf.net/sfu/intel-sw-dev >>>> >>>> ------------------------------ >>>> >>>> _______________________________________________ >>>> PyMOL-users mailing list >>>> PyMOL-users@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>>> >>>> >>>> End of PyMOL-users Digest, Vol 45, Issue 9 >>>> ****************************************** >>>> >>> >>> >>> >>> >>> ------------------------------ >>> >>> Message: 4 >>> Date: Thu, 18 Feb 2010 22:33:14 -0500 >>> From: "Kent Rossman" <kross...@med.unc.edu> >>> Subject: [PyMOL] Save movie not working >>> To: pymol-users@lists.sourceforge.net >>> Message-ID: <4b7e067a.7070...@med.unc.edu> >>> Content-Type: text/plain; charset=iso-8859-1; format=flowed >>> >>> Hi Delano, >>> >>> When I try to save an MPEG from the save movie menu, pymol works on >>> writing out the movie, then i get an error that says mpeg_encode.exe >>> has >>> encounteres a problem and has to close. A file is written with 0 >>> bytes. There was also an error that mpeg_encode was being used by >>> another file/program...I think. Can you help? >>> >>> Thanks, >>> kr >>> >>> -- >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> Kent Rossman, Ph.D. >>> Research Assistant Professor >>> Department of Pharmacology >>> Lineberger Comprehensive Cancer Center >>> UNC-Chapel Hill, CB 7295 >>> Chapel Hill, NC 27599 >>> >>> Tel: 919-962-1057 >>> Fax: 919-966-0162 >>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> >>> >>> >>> >>> >>> >>> ------------------------------ >>> >>> ------------------------------------------------------------------------------ >>> Download Intel® Parallel Studio Eval >>> Try the new software tools for yourself. Speed compiling, find bugs >>> proactively, and fine-tune applications for parallel performance. >>> See why Intel Parallel Studio got high marks during beta. >>> http://p.sf.net/sfu/intel-sw-dev >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> PyMOL-users mailing list >>> PyMOL-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/pymol-users >>> >>> >>> End of PyMOL-users Digest, Vol 45, Issue 10 >>> ******************************************* >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> 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 Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ 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
