Re: [PyMOL] Color states as rainbow

Hi Jacob, I fixed the color_obj script in the wiki, it had a bug. Btw. I like Tsjerk's suggestion best, using b-factors. Cheers, Thomas Jacob Keller wrote, On 12/19/11 03:38: > Dear Pymol list, > > I have been trying to color the states in a morph by spectrum to try > to show the motion in

[PyMOL] Annual CCP4 summer school in USA, at APS, June 19-26

Dear Colleagues, We are pleased to announce the fifth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Title: "CCP4 school: From data collection to structure refinement and beyond" D

[PyMOL] Problem with open source pymol

Hi Everyone, I've compiled and installed pymol 1.3 on my Mac (OS 10.6 running Snow Leopard), but pymol keeps crashing. The compilation looks clean, so I have no idea why it's giving me trouble. I have pasted the details below. Any help would be much appreciated. Thanks! ~Lauren Python 2.5

Re: [PyMOL] Problem with open source pymol

2011-12-19 12:32:21.901 Python[243:5d03] *** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason*: '-[GLUTApplication _setup:]:* unrecognized -- Do you have glut installed ? http://www.pymolwiki.org/index.php/Linux_Install#Requiremen

[PyMOL] Center of screen?

Hi all Is it possible to put a crosshairs at the center of the viewing area that always shows where the center is? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder --

Re: [PyMOL] Center of screen?

Hi Francis, you could use a pseudoatom (or CGO object) and a callback that constantly updates the position. python from pymol import cmd cmd.pseudoatom('crosshair', pos=(0,0,0)) cmd.show_as('nonbonded', 'crosshair') def crosshair_put_center(): t = cmd.get_position() m = [1, 0, 0, t[0],

Re: [PyMOL] Color states as rainbow

Jacob Keller wrote, On 12/19/11 19:04: > Yes, now it works perfectly--thanks very much! Also, did you see some > advantage of doing the b-factor idea over your script, or just a good > parallel strategy? it's just a good parallel strategy. And is done with 2 lines instead of loading an extra scri

Re: [PyMOL] Problem with open source pymol

Yes, I have GLUT installed (I'm using the framework), and I rerouted everything to make sure it was pointing to the right path. After doing that, I rebuilt and got a new error: Python 2.5.4 (r254:67916, Aug 1 2011, 15:52:49) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright",

Re: [PyMOL] Color states as rainbow

Yes, now it works perfectly--thanks very much! Also, did you see some advantage of doing the b-factor idea over your script, or just a good parallel strategy? Jacob On Mon, Dec 19, 2011 at 2:41 AM, Thomas Holder wrote: > Hi Jacob, > > I fixed the color_obj script in the wiki, it had a bug. > > B

[PyMOL] Pymol Crashes Despite Plenty of Extra Memory

Dear Pymol Users, I have 6 GB of RAM, but I am still getting crashes when I try to render my 30-state figure, even when I don't raise the hash_max (lowering it makes it take really long). When I look at the task manager to see how much RAM is being used, it still is very far from being maxed out,

Re: [PyMOL] Color states as rainbow

Cleaned up a little, this would make a nice simple addition to the PyMOLWiki script library. Cheers, -- Jason On Mon, Dec 19, 2011 at 2:13 AM, Takanori Nakane wrote: > Hi Jacob, > > The following command will make blue to purple spectrum. >  (please type in one line) > > for i in range(1 + cmd.