[PyMOL] python as a satellite virus
Coincidently that was the exact same program that hosed my python installation too. I had set up my computer to run the python based AutoDock Tools interface to the docking program AutoDock. The installer for this program puts its own copy of python as a subdirectory in the main application directory and adds some environment variables to the .cshrc file. Apparently, some variable created here affected other python based apps. When I commented these out and opened a new xterm and ran pymol, everything worked normally. Moreover, my attempts to re-engineer the AutoDock installation ended in a complete morass. This is a great reason for installation software to at least allow you the option of using your already installed system python.
Re: [PyMOL] python as a satellite virus
At 10:50 AM -0700 4/30/03, wgsc...@chemistry.ucsc.edu wrote: Coincidently that was the exact same program that hosed my python installation too. I had set up my computer to run the python based AutoDock Tools interface to the docking program AutoDock. The installer for this program puts its own copy of python as a subdirectory in the main application directory and adds some environment variables to the .cshrc file. Apparently, some variable created here affected other python based apps. When I commented these out and opened a new xterm and ran pymol, everything worked normally. Moreover, my attempts to re-engineer the AutoDock installation ended in a complete morass. This is a great reason for installation software to at least allow you the option of using your already installed system python. Here's what I told my students. It seemed like a reasonable solution. _ It appears that the problem was introduced by the installation of ADT. The ADT installer puts some lines in your .cshrc file that prevents pymol from working properly. So here is a solution that worked for me. Take out the ADT lines and put them into a separate text file--say call it ADTenv.csh. If you open a new xterm, pymol should not work properly. If you want to run ADT, open a new xterm and source ADTenv.csh (no quotes). Then run adt (no quotes) from this window. _ Although I didn't try it, I assume that you can't run pymol from that xterm once you've run the ADTenv.csh script. TG -- _ Terry M. Gray, Ph.D., Computer Support Scientist Chemistry Department, Colorado State University Fort Collins, Colorado 80523 gr...@lamar.colostate.edu http://www.chm.colostate.edu/~grayt/ phone: 970-491-7003 fax: 970-491-1801
RE: [PyMOL] RE: Stereo pictures, light vector and shadows
Yep, I blew it -- neglected to check my work. Scratch all of my previous emails on the subject. The following function (turn_y_light.py) will correctly rotate the light in order to offset the effect of turn y,# def turn_y_light(rot): # assuming rot has angle in degrees rot_rad = math.pi*rot/180.0 (X0,Y0,Z0)=cmd.get_setting_tuple(light)[1] X1= X0*math.cos(rot_rad) + Z0*math.sin(rot_rad) Y1= Y0 Z1= Z0*math.cos(rot_rad) - X0*math.sin(rot_rad) cmd.set(light,[X1,Y1,Z1]) sample usage: # first, load the function from a .py file run turn_y_light.py # now use it... turn y,3 turn_y_list(3) ray png image1.png turn y,-6 turn_y_light(-6) ray png image2.png Sorry for the confusion! Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Anthony Duff Sent: Tuesday, April 29, 2003 9:08 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] RE: Stereo pictures, light vector and shadows Warren's script is not quite right. The value -0.902 is not correct. Apparently, my picture, with a stick peptide casting a shadow on the inner surface of a deep crevice, is particularly demanding. I have done the vector calculations. See the attached excel worksheet for light vectors for any desired stereo angle. I am using the script below. It produces perfect shadows and reflections. turn y, 3 set light=[-0.43709,-0.34800,-0.82937] ray 1120,818 png image.l.png turn y, -6 set light=[-0.34800,-0.34800,-0.87051] ray 1120,818 png image.r.png Anthony At 05:10 AM 24/04/2003, Warren L. DeLano wrote: In the script I just posted, I used unit vectors to specify the light direction and simply rotated that vector by 6 degrees. The first vector is merely [-0.4,-0.4,-1.0] normalized. The second is that same vector rotated 6 degrees about the Y axis. I then loaded the output into Illustrator and was able to view both cross-eye and wall-eye stereo pairs with clean shadows. Try using this sequence to create your stereo pair: set light=[-0.348,-0.348,-0.870] ray png image1.png turn y,6 set light=[-0.437,-0.348,-0.902] ray png image2.png turn y,-6 Cheers, Warren -- Anthony Duff Postdoctoral Fellow School of Molecular and Microbial Biosciences Biochemistry Building, G08 University of Sydney, NSW 2006 Australia Phone. 61-2-9351-7817 Fax. 61-2-9351-4726 --
RE: [PyMOL] RE: Stereo pictures, light vector and shadows
(sorry, bad day continues) fixed type in the sample usage: # first, load the function from a .py file run turn_y_light.py # now use it... turn y,3 turn_y_light(3) ray png image1.png turn y,-6 turn_y_light(-6) ray png image2.png -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Warren L. DeLano Sent: Wednesday, April 30, 2003 1:54 PM To: 'Anthony Duff'; pymol-users@lists.sourceforge.net Cc: f.h.j.van.hoe...@chem.rug.nl Subject: RE: [PyMOL] RE: Stereo pictures, light vector and shadows Yep, I blew it -- neglected to check my work. Scratch all of my previous emails on the subject. The following function (turn_y_light.py) will correctly rotate the light in order to offset the effect of turn y,# def turn_y_light(rot): # assuming rot has angle in degrees rot_rad = math.pi*rot/180.0 (X0,Y0,Z0)=cmd.get_setting_tuple(light)[1] X1= X0*math.cos(rot_rad) + Z0*math.sin(rot_rad) Y1= Y0 Z1= Z0*math.cos(rot_rad) - X0*math.sin(rot_rad) cmd.set(light,[X1,Y1,Z1]) sample usage: # first, load the function from a .py file run turn_y_light.py # now use it... turn y,3 turn_y_list(3) ray png image1.png turn y,-6 turn_y_light(-6) ray png image2.png Sorry for the confusion! Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Anthony Duff Sent: Tuesday, April 29, 2003 9:08 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] RE: Stereo pictures, light vector and shadows Warren's script is not quite right. The value -0.902 is not correct. Apparently, my picture, with a stick peptide casting a shadow on the inner surface of a deep crevice, is particularly demanding. I have done the vector calculations. See the attached excel worksheet for light vectors for any desired stereo angle. I am using the script below. It produces perfect shadows and reflections. turn y, 3 set light=[-0.43709,-0.34800,-0.82937] ray 1120,818 png image.l.png turn y, -6 set light=[-0.34800,-0.34800,-0.87051] ray 1120,818 png image.r.png Anthony At 05:10 AM 24/04/2003, Warren L. DeLano wrote: In the script I just posted, I used unit vectors to specify the light direction and simply rotated that vector by 6 degrees. The first vector is merely [-0.4,-0.4,-1.0] normalized. The second is that same vector rotated 6 degrees about the Y axis. I then loaded the output into Illustrator and was able to view both cross-eye and wall-eye stereo pairs with clean shadows. Try using this sequence to create your stereo pair: set light=[-0.348,-0.348,-0.870] ray png image1.png turn y,6 set light=[-0.437,-0.348,-0.902] ray png image2.png turn y,-6 Cheers, Warren -- Anthony Duff Postdoctoral Fellow School of Molecular and Microbial Biosciences Biochemistry Building, G08 University of Sydney, NSW 2006 Australia Phone. 61-2-9351-7817 Fax. 61-2-9351-4726 -- --- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
RE: [PyMOL] surface
Molecular (a discrete approximation to the Connolly surface). -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dennis Wolan Sent: Tuesday, April 29, 2003 2:42 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface Dear all, This has probably been asked a thousand times, but is the default surface representation a molecular surface or a solvent accessible surface? Thanks in advance, Dennis
