[PyMOL] Latency in updating pointer from external input device
We are attempting to use a set of external input devices (wiimotes) to allow interaction with pymol and are achieving this by having a seperate thread running that talk to the wiimote over bluetooth and sends commands to pymol when appropriate. Commands such as rotate or move the view go through at a reasonably high framerate but any time we try to update the position of a pointer(via a shared variable) that we are drawing in a pymol opengl callback the framerate goes way down. Has anyone tried to do something similar to this (draw and move around an additional pointer for selection purposes) and had any luck in finding a way to get it to achieve reasonable performance. thanks, Aaron -- 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
Re: [PyMOL] feature request
Could the connect_mode setting be better documented? The current documentation doesn't say much about what that setting does. nick On Fri, Mar 12, 2010 at 12:08, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Nicolas, > > Try: > > set connect_mode, 2 > load yourXYZ.xyz, discrete=1 > > -- Jason > > On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock > wrote: > > Please find attached an example xyz file. > > > > nick > > > > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock > wrote: > >> > >> When I load an xyz file with several frames (for example the result of > an > >> MD simulation) I find that pymol calculates and sets the bonds only > using > >> the initial frame. For frames > 1 the bonds are not recalculated. The > only > >> "work around" I found is to load(..., multiplex=1) which loads the > frames > >> into separate objects. But now I can not play the MD trajectory as a > movie. > >> > >> I would like to suggest that this feature be added to pymol so that MD > >> trajectories can be played with proper bonding for all frames. > >> > >> Thanks > >> > >> nick > >> > > > > > > > -- > > 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 > -- 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
Re: [PyMOL] feature request
Great, that works! On Fri, Mar 12, 2010 at 12:08, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Nicolas, > > Try: > > set connect_mode, 2 > load yourXYZ.xyz, discrete=1 > > -- Jason > > On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock > wrote: > > Please find attached an example xyz file. > > > > nick > > > > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock > wrote: > >> > >> When I load an xyz file with several frames (for example the result of > an > >> MD simulation) I find that pymol calculates and sets the bonds only > using > >> the initial frame. For frames > 1 the bonds are not recalculated. The > only > >> "work around" I found is to load(..., multiplex=1) which loads the > frames > >> into separate objects. But now I can not play the MD trajectory as a > movie. > >> > >> I would like to suggest that this feature be added to pymol so that MD > >> trajectories can be played with proper bonding for all frames. > >> > >> Thanks > >> > >> nick > >> > > > > > > > -- > > 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 > -- 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
Re: [PyMOL] feature request
Nicolas, Try: set connect_mode, 2 load yourXYZ.xyz, discrete=1 -- Jason On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock wrote: > Please find attached an example xyz file. > > nick > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote: >> >> When I load an xyz file with several frames (for example the result of an >> MD simulation) I find that pymol calculates and sets the bonds only using >> the initial frame. For frames > 1 the bonds are not recalculated. The only >> "work around" I found is to load(..., multiplex=1) which loads the frames >> into separate objects. But now I can not play the MD trajectory as a movie. >> >> I would like to suggest that this feature be added to pymol so that MD >> trajectories can be played with proper bonding for all frames. >> >> Thanks >> >> nick >> > > > -- > 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 -- 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
Re: [PyMOL] feature request
I should mention that the first 3 columns are the cartesian coordinates in Angstroms, and the last 3 columes the forces in eV/A. On Fri, Mar 12, 2010 at 11:50, Nicolas Bock wrote: > Please find attached an example xyz file. > > nick > > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote: > >> When I load an xyz file with several frames (for example the result of an >> MD simulation) I find that pymol calculates and sets the bonds only using >> the initial frame. For frames > 1 the bonds are not recalculated. The only >> "work around" I found is to load(..., multiplex=1) which loads the frames >> into separate objects. But now I can not play the MD trajectory as a movie. >> >> I would like to suggest that this feature be added to pymol so that MD >> trajectories can be played with proper bonding for all frames. >> >> Thanks >> >> nick >> >> > -- 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
Re: [PyMOL] feature request
Please find attached an example xyz file. nick On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote: > When I load an xyz file with several frames (for example the result of an > MD simulation) I find that pymol calculates and sets the bonds only using > the initial frame. For frames > 1 the bonds are not recalculated. The only > "work around" I found is to load(..., multiplex=1) which loads the frames > into separate objects. But now I can not play the MD trajectory as a movie. > > I would like to suggest that this feature be added to pymol so that MD > trajectories can be played with proper bonding for all frames. > > Thanks > > nick > > HCN_to_CHN.xyz Description: Protein Databank data -- 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
[PyMOL] feature request
After editing a molecule it can happen that the bonds that used to be there don't all make sense anymore, for example, because I moved an atom pretty far away from its original place. It would be nice if one could call a function to force pymol at some point to recalculate the bonds in the molecule. Unfortunately there is currently no "rebond" function. I would like to suggest that it be added. Thanks nick -- 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
[PyMOL] feature request
When I load an xyz file with several frames (for example the result of an MD simulation) I find that pymol calculates and sets the bonds only using the initial frame. For frames > 1 the bonds are not recalculated. The only "work around" I found is to load(..., multiplex=1) which loads the frames into separate objects. But now I can not play the MD trajectory as a movie. I would like to suggest that this feature be added to pymol so that MD trajectories can be played with proper bonding for all frames. Thanks nick -- 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
Re: [PyMOL] feature request?
Nick, Please email bug reports and feature suggestions to h...@schrodinger.com. CC the list if you like. Cheers, -- Jason On Fri, Mar 12, 2010 at 11:17 AM, Nicolas Bock wrote: > Hello list, > > what's the mechanism for submitting feature requests or bug reports? To this > list? > > nick > > > -- > 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 -- 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
[PyMOL] feature request?
Hello list, what's the mechanism for submitting feature requests or bug reports? To this list? nick -- 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
