[PyMOL] interlaced and checkerboard stereo problems
We are having problems getting interlaced and checkerboard stereo to work with the latest incentive builds. On both windows xp and OS X 10.6 we can enable both byrow/bycolumn/checkerboard stereo and in all cases we see two copies of the molecule but no checkerboard or interlaced pattern. In both these cases we are using nvidia graphics cards. The only case where we have seen it working is on windows 7 with an ati graphics card. Is anyone experiencing similar problems and/or are their any known bugs. thanks, Aaron -- ___ 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] interlaced and checkerboard stereo problems
As a further twist, the zalman build works fine for both interlaced and checkerboard. Aaron On Fri, May 14, 2010 at 4:38 PM, aaron bryden bry...@wisc.edu wrote: We are having problems getting interlaced and checkerboard stereo to work with the latest incentive builds. On both windows xp and OS X 10.6 we can enable both byrow/bycolumn/checkerboard stereo and in all cases we see two copies of the molecule but no checkerboard or interlaced pattern. In both these cases we are using nvidia graphics cards. The only case where we have seen it working is on windows 7 with an ati graphics card. Is anyone experiencing similar problems and/or are their any known bugs. thanks, Aaron -- ___ 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-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] stereo stretching on 3d HDTV
We are trying to use pymol on our new 3D HDTV that accepts a single frame side by side stereo format and stretches the two sides into a full frame. This works somewhat well with Pymol's geowall setting but the image is (of course) stretched. Is their any way to make PyMOL squeeze each side of the geowall image so that when the display restreches it the desired result will be achieved. thanks, Aaron -- ___ 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] 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#174; 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] Compilation issues on Win32 vs2008
We are attempting to compile pymol on windows so that it is compiled against the version of python that we use in all of our other software (due to our IT situation this would make our plugin development substantially easier). Our version of python is 2.6. We are using the distutils method where our command to compile is 'python.exe setup.py build' After dealing with all of the dependencies and fixing os_predef.h to ask the linker to use recent versions of libraries it almost completely compiled. We are stuck at the end with the following link error: mfcs90.lib(nolib.obj) : error LNK2001: unresolved external symbol int __cdecl _ AfxInitManaged(void) (?_AfxInitManaged@@YAHXZ) mfcs90.lib(stdafx.obj) : error LNK2001: unresolved external symbol int __cdecl _AfxInitManaged(void) (?_AfxInitManaged@@YAHXZ) We have looked for a way to get this symbol in our program and are at a loss. Google points to precompiled header issues but as far as we can tell, distutils is not making use of precompiled headers. If anyone has had any experience with this or any suggestions it would be greatly appreciated. thanks, aaron bryden -- 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
[PyMOL] checkerboard stereo
Are their any plans to improve checkerboard stereo support for 3D DLP hdtvs any time soon in the incentive builds. for more info look at: http://www.dlp.com/hdtv/3-d_dlp_hdtv.aspx thanks, aaron bryden
[PyMOL] resize to span 2 outputs on OS X
Does anyone know of a way to reliably convince pymol to span exactly 2 video outputs in a scripted fashion on OS X for the purpose of geowall stereo. If I use the viewport command, this causes the window to stretch beyond the edge of the screen because of the user interface that is part of the opengl window. Currently in order to use pymol on our geowall, users have to maximize pymol on one window and drag it across the other screen. Is their a better solution? thanks, Aaron Bryden
Re: [PyMOL] real time editing/moving of molecular structure from scripting interface
Thank you very much, this works much faster than cmd.alter_state. On 10/9/07, Tsjerk Wassenaar tsje...@gmail.com wrote: #--- Python proof e-mail ;) --- # Hi Aaron, # You can get to the coordinates in the following way: # First make a model from the selection you want to work on: sel = cmd.get_model( object ) # Then you can get to the coordinates and modify them without affecting the view: for i in range(len(sel.atom)): sel.atom[i].coord = transform( sel.atom[i].coord ) # When all is done, you can load the coordinates back into the model: cmd.load_model( sel, object, state ) # Hope it helps, # Tsjerk #-- # Tsjerk A. Wassenaar, Ph.D. # Junior UD (post-doc) # Biomolecular NMR, Bijvoet Center # Utrecht University # Padualaan 8 # 3584 CH Utrecht # The Netherlands # P: +31-30-2539931 # F: +31-30-2537623
[PyMOL] real time editing/moving of molecular structure from scripting interface
I want to apply a bunch of arbitrary changes to the positions of atoms via the scripting interface and when I am done force it to redraw the molecule in the position i specified (or the next time a redraw happens because animation is on, draw the molecule in the new position) without having to completely rebuild the representation (i realize this won't be possible with surface and mesh but don't see any reason for it not to work with cartoon, stick or spheres), while maintaining interactivity (the plugin I am developing has various sliders that affect the changes applied to the molecule and I want the molecule to move as the sliders move). Is this possible or will i have to delve deeper into pymol and extend an interface to do this? Currently I am doing this with cmd.alter_state, is their a better way. I know this must be possible on some level since it is achieved in the sculpting demo and when editing the molecular structure w/ the mouse. thanks in advance, aaron bryden Phillips Lab University Of Wisconsin Madison
[PyMOL] vrml broken normals
normals appear to be still broken in VRML export. I have attached a simple test case that demonstrates this. The pdb file attached contains 1 atom at the origin. To reproduce the wrl file that I have attached, set the quality to best performance, turn on surface rendering of the molecule and export the wrl file. The resulting wrl file clearly has wrong normals both looking at it by hand an opening it up in deep exploration version 5 and looking at the normals. This is with the latest incentive build on OS X. aaron
[PyMOL] vrml export normals
Has anyone had good luck with the VRML export. It seems that there is a problem with the normals that are exported in some cases. Can anyone recommend a VRML viewer that works well with the exported files. aaron
[PyMOL] scene export
Does anyone know of the best way to get a scene export of all polygons currently being used? I am not afraid to modify the pymol source and have done so for other custom projects. The vrml export option is very much appreciated but exporting stick models has the unfortunate consequence that the bonds are exported as cylinders as opposed to polygons, which results in the vrml interpreter rendering the sticks with lots of polygons. Has anyone looked into solutions for this problem other than getting your vrml importer to use more coarse primitives? Aaron
[PyMOL] Sequence view size
Is their any way to get the size in pixels of the sequence view like their is of the internal gui, or the size in pixels of the space actually used for drawing? I know that glGetDouble(GL_VIEWPORT) but this doesn't take into account the internal gui or the sequence view. I can find a way to get the size of the internal gui but not the sequence view. thanks, Aaron
[PyMOL] Wall Eye stereo widgets
Hey, Is their any way to make the wall eye stereo mode draw the various controls for each eye. Specifically I am talking about the panel on the right and the sequence display/selection control. Where in the code tree should I consider looking in order to add this functionality. Also does a developers manual exist anywhere? Or is it pretty much read the code in order to understand the structure. Thank you for your time, Aaron
