[PyMOL] Displaying .kont files / Grid Users
Hi Folks ! I was very happy when I saw the possibility in Pymol to load and visualize moe states. I' ve been working with the computer program Grid for nearly two years now and I always have had incredible problems to display the molecular interaction fields (Mif's) . The Grid Viewer supported by Moldiscovery is not supported by current Ubuntu distribution due very old / lacking libraries. With Moe and an additional svl script it is possible to convert the kont file to a moe state so that a subsequent pymol read -in is possible. (I think this way isn't really straightforward :-() Are there any others of you working with grid / and / or having this problem? Would it be possible to implement a direct kont -read in option in pymol?( it's only a forcefield value and x/y/z data. Best regards, florian -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] states for distance objects
I have a set of objects generated by "distance" commands through which I would like to cycle, for example with the movie controls. Using "create" to generate individual states of a single object does not work as the distance objects do not contain atoms. Is there a solution to this problem? Many thanks, Bernd -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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] states for distance objects
Hello Bernd, The trick is to create the distance objects using atoms already present in the states you wish the distances to occupy. For example: # load NMR structure fetch 1nmr, async=1 # measure N to C distance in each frame distance demo, 1/N, 85/C # play set movie_fps, 1 mplay Cheers, Warren From: Kuhn, Bernd [mailto:bernd.k...@roche.com] Sent: Friday, August 14, 2009 5:04 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] states for distance objects I have a set of objects generated by "distance" commands through which I would like to cycle, for example with the movie controls. Using "create" to generate individual states of a single object does not work as the distance objects do not contain atoms. Is there a solution to this problem? Many thanks, Bernd -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Displaying .kont files / Grid Users
Florian, Can you convert the files to Insight GRID ".grd" format? PyMOL can read those files directly. Alternatively, dependeing upon complexity of the task, you might be able to study the SVL .kont reader and create a Python equivalent for use with PyMOL. Cheers, Warren > -Original Message- > From: Florian Koelling [mailto:florian.koell...@tu-bs.de] > Sent: Friday, August 14, 2009 5:04 AM > To: PyMOL-users@lists.sourceforge.net > Subject: [PyMOL] Displaying .kont files / Grid Users > > Hi Folks ! > > I was very happy when I saw the possibility in Pymol to load and > visualize moe states. I' ve been working with the computer program Grid > for nearly two years now and > I always have had incredible problems to display the molecular > interaction fields (Mif's) . > > The Grid Viewer supported by Moldiscovery is not supported by current > Ubuntu distribution due very old / lacking libraries. > > > With Moe and an additional svl script it is possible to convert the kont > file to a moe state so that a subsequent pymol read -in is possible. > (I think this way isn't really straightforward :-() > > > Are there any others of you working with grid / and / or having this > problem? > Would it be possible to implement a direct kont -read in option in > pymol?( it's only a forcefield value and x/y/z data. > > > Best regards, > > florian > > -- > > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30- > Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > ___ > 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 > > > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] AxPyMOL Updated: .MAE and .MOE support.
FYI, for Windows users who like to live "on the edge"... AxPyMOL is the PyMOL Active Control, which makes it possible to display live molecular content, including PyMOL PSE and PSW files inside of PowerPoint (on Windows only). Because we are still having trouble getting this Windows-based component to work perfectly (i.e. without crashing), we are continuing to give away a version of AxPyMOL as a FREE, but UNSUPPORTED extra capability for use AT YOUR OWN RISK. Today we posted an updated 1.2r1 version of AxPyMOL designed to work with PyMOL 1.2 session and show files. You can download it from: http://delsci.com/axpymol (file: axpymol-1_2r1-free-090814.msi) . Note that AxPyMOL is currently intended for use inside PowerPoint only, with external data files stored locally in the same folder as your presentation. After installation, use the Control Toolbox -> More Controls button to select and drag out an AxPyMOL rectangle in your slide, and then follow the instructions shown onscreen. The PowerPoint Control Toolbox can be displayed via the PowerPoint "View" menu -> Toolbars option. By the way, one particularly useful aspect of AxPyMOL is that it can directly read and display .MAE and .MOE files. So, if you use Chemical Computing Group's M.O.E. or Schrodinger's Maestro, then you should be able to load and interact with your .MOE and .MAE files directly inside of PowerPoint using AxPyMOL. We need more feedback on how the component works out in the real-world, so thanks in advance to those of you who try AxPyMOL and report back! Cheers, Warren PS. With Office 2007, in order to retain placeholder images, please save your presentation in .PPT not .PPTX format. -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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
