[PyMOL] how to make molecule B move around molecule A

Dear Pymolers, I started to use Pymol(0.86) from last week and am still new to it. A complex at my hand contains mol A + B. MolA is hexamer (A1-A6) and B a monomer. Mol B modifies mol A one by one (please see the diagram below). when making a movie, is there any easy way to move B around

[PyMOL] RE: Stereo pictures, light vector and shadows

Scott, PyMOL's lighting model is merely a direction, not a point. The default direction vector isn't even normalized to unit length. 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

[PyMOL] Stereo pictures, light vector and shadows

Warren, Could you explain the values for the set light command? It appears the default values are [-0.4,-0.4,-1.0] how do the values below correspond to a 6 degree rotation of the light source? Thanks, Scott On Wednesday, April 23, 2003, at 08:59 AM, Warren L. DeLano wrote: Yo

RE: [PyMOL] Stereo pictures, light vector and shadows

Yow, good point! I'm surprise none of us realized this before : ) You need to change the direction of the light 6 degrees as well. 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

RE: [PyMOL] surface charge?

Camille, This capability exists in the development version, but isn't ready for prime-time yet. Look for it in the next release. In the meantime, you might try using raster3d to render your grasp surface, via its "ungrasp" tool. http://www.bmsc.washington.edu/raster3d/html/r3d_filters.html#g

RE: [PyMOL] RGB2CMYK

Camille, Gil Prive posted a set of CMYK colors before: http://sourceforge.net/mailarchive/message.php?msg_id=2299470 My only comment was that you don't need to add a preceeding underscore to his color names -- you can simply redefine the ones which already exist. set_color _green= [0.00 , 0.53

Re: [PyMOL] RGB2CMYK

On Wednesday, April 23, 2003, at 06:30 AM, wrote: can anyone direct me to a url with RGB colours (in the format below) and their CMYK equivalents? At the moment I'm messing around with the following kind of thing Hi Camille, One free utility I found very useful for this kind of things

[PyMOL] RGB2CMYK

Hi, can anyone direct me to a url with RGB colours (in the format below) and their CMYK equivalents? At the moment I'm messing around with the following kind of thing set_color cyan2=[0.7, 1.0, 1.0] I need to use a cyan color in a figure but unfortunately this becomes very dark when th

[PyMOL] surface charge?

Hi Warren, I'm using PyMol to make the figures in a paper I am currently writing. I know that pymol can generate surfaces at the moment but not charge. Is there any way to colour a surface by charge in pymol using charges calculated in grasp? ...or can I import a grasp surface? I heard that t

RE: [PyMOL] Will a faster graphics card speed up ray tracing?

On Tue, 22 Apr 2003, Nat Echols wrote: > Would the results be of interest to others on the list? Yes, please post! I have some old Itaniums (actually, 8 dual Itaniums), and I'll be happy to try PyMOL on one of them. Kneth -- Kenneth Geisshirt - Principal Scientist Silex Science ApS, Trekronerg

RE: [PyMOL] Transparency in residues

Mads, That feature didn't make it into the 0.86 release, but it is in the current development version. Look for it in the next release. Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -