RE: [PyMOL] pymol without GL
Not right now... In order to build PyMOL without linking to real GL libraries, you'd either need a fake copy of the GL API, or "#define" out all of the gl calls in PyMOL (many hours of work). Sorry! Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -Original Message- > From: Nathaniel Echols [mailto:n...@mail.csb.yale.edu] > Sent: Tuesday, July 16, 2002 12:09 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] pymol without GL > > > > quick question: I'm trying to do batch jobs on a server. Obviously, > there's no X or OpenGL installed. Is there any way to build > PyMOL without > any graphical frontend, and just use it as a raytracer? I > don't want to > go through the trouble of adding in these libraries... > > thanks, > Nat > > > > --- > This sf.net email is sponsored by: Jabber - The world's > fastest growing > real-time communications platform! Don't just IM. Build it in! > http://www.jabber.com/osdn/xim > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
[PyMOL] Bug in CGO cylinder drawing code?
Warren, I have found a CGO-drawing problem for which I cannot find a solution. I've been trying to perfect my script for drawing symmetry axes of crystal structures. I noticed that the script wasn't drawing all of the axes that it should have (i.e. not all of those that were listed by the script). I did some investigating of the behaviour by writing the CGO objects out to a file and then editing it down to just a few cylinder objects. The grand conclusion, is that if you create a CGO cylinder that goes from 0,0,0 to x,-x,x (or parallel to that direction) apparently no matter what the value of x, it does not appear in the graphics window. Here are some samples. First I was trying to draw the four 3-fold axes of space group P23: #! /usr/bin/python from pymol.cgo import * from pymol import cmd ax = [ CYLINDER, 0.0, 0.0, 0.0, -30.0, -30.0, 30.0, 0.2, 1.0, 0.5, 0.0, 1.0, 0.5, 0.0, CYLINDER, 0.0, 0.0, 0.0, -30.0, 30.0, 30.0, 0.2, 1.0, 0.5, 0.0, 1.0, 0.5, 0.0, CYLINDER, 0.0, 0.0, 0.0, 30.0, -30.0, 30.0, 0.2, 1.0, 0.5, 0.0, 1.0, 0.5, 0.0, CYLINDER, 0.0, 0.0, 0.0, 30.0, 30.0, 30.0, 0.2, 1.0, 0.5, 0.0, 1.0, 0.5, 0.0, ] cmd.load_cgo(ax,'ax') but the 3rd of these cylinders does not appear. So I altered one of the end-point values ever so slightly: ax2 = [ CYLINDER, 0.0, 0.0, 0.0, -30.0, -30.0, 30.0, 0.2, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, CYLINDER, 0.0, 0.0, 0.0, -30.0, 30.0, 30.0, 0.2, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, CYLINDER, 0.0, 0.0, 0.0, 30.1, -30.0, 30.0, 0.2, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, CYLINDER, 0.0, 0.0, 0.0, 30.0, 30.0, 30.0, 0.2, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, ] cmd.load_cgo(ax2,'ax2') Now the 3rd cylinder appears. Similarly, changing one of the starting points, (X, Y or Z -- doesn't matter which) and the cylinder will appear. I tried rearranging the order of the cylinders and it always seems to be that particular cylinder that is not drawn. So finally I tried drawing individual cylinders and found that for example, the following also will not appear: ax3 = [CYLINDER, 0.0, 0.0, 0.0, 2., -2.0, 2.0, 0.5, 0.0, 1.0, 1.0, 0.0, 1.0, 1.0] cmd.load_cgo(ax3,'ax3') Changing any X, Y or Z value for either the starting or end point of the cylinder will make the cylinder reappear. Finally, cylinders from (0,0,0) to (-x,x,-x) and from (x,-x,x) to (0,0,0) also do not appear (i.e. the same direction). The presence of (0,0,0) as one of the starting or end points doesn't matter: (2.0, 2.0, 2.0) to (4.0, 0.0, 4.0) also does not appear. There is something strange about this (1,-1, 1) direction! I have found this to be true with the CVS version as well as the 0.78 version (both running under Linux) and the CVS and 0.68 version under IRIX. It doesn't appear to matter what display settings are set. But the cylinder does appear when the image is ray-traced! I don't think there is anything that I'm doing wrong here, but if you have a clue, I'd be very interested! Cheers, Robert -- Robert L. Campbell, Ph.D. http://biophysics.med.jhmi.edu/rlc r...@k2.med.jhmi.eduphone: 410-614-6313 Research Specialist/X-ray Facility Manager HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
[PyMOL] GUI problem on Win2000
Hello everybody At home, I run pymol on Debian/Linux without any problems. However, at university, we only have windows machines. So I downloaded and installed Python2.2.1, ActiveTCL 8.3.4.3 and, of course, Pymol 0.82. So far, I can run (and use) pymol giving commands in the OpenGL window, but the GUI (which depends on Tcl/Tk) does not appear. The startup window gives the following error message: self.root = Tk() File "C:\PROGRA~1\PYTHON~1\Lib\lib-tk\Tkinter.py", line 1487, in __init__ self.tk = _tkinter.create(screenName, baseName, className) TclError: Can't find a usable init.tcl in the following directories: {C:\python21\tcl\tcl8.3 (guessing)} {} {C:\python21\tcl\tcl8.3 (guessing)} C:/python21/tcl/tcl8.3 C:/PROGRA~1/PYTHON~1/lib/tcl8.3 c:/programme/lib/tcl8.3 c:/lib/tcl8.3 c:/lib/tcl8.3/library c:/library c:/../tcl8.3/library ../tcl8.3/ library So, what can I do to help pymol finding init.tcl and display the GUI? Thanks, joerg PS.: Please CC: to me, as I'm not subscribed to this list. -- Did you know that if you play a Windows 2000 cd backwards, you will hear the voice of Satan? That's nothing! If you play it forward, it'll install Windows 2000. GMX - Die Kommunikationsplattform im Internet. http://www.gmx.net
[PyMOL] Fusing objects
I have created a number of objects using "symexp" to represent a crystal structure. I now need to recompute the bonds to display molecules split across periodic copies. 1. Am I correct in understanding that I need to "FUSE" all the objects into one to display all inter-object bonds? 2. Is there a quick and general way of doing this? The documentation suggests that I have to pick every atom pair to do this, which would be cumbersome to say the least. I'm sure I must be missing something. Thanks Keith Refson -- Dr Keith Refson, Building R3 Rutherford Appleton Laboratory Chilton Didcot Oxfordshire OX11 0QX T: 01235 446652 K.Refson@ F: 01235 445720 @rl.ac.uk