[PyMOL] how to get the mouse information

Hi, I am wondering how to get the mouse information from Pymol. For example, when moving the molecule, how to actually read the start and end position from the mouse? Thanks a lot! Joy __ Yahoo! Music Unlimited Access over 1 million songs. Try

[PyMOL] How can I get the color ramp to show up in raytraced images?

Hi, When I use the APBS plugin to look at electrostatic potentials, I get a color ramp at the bottom of the window (e.g. red and -1 on the left, blue and +1 on the right) that shows the color scale that I'm using. When I raytrace, that ramp goes away. How can I make it show up in the

RE: [PyMOL] How can I get the color ramp to show up in raytraced images?

Michael, There's a scaling bug for raytracing the ramp in perspective mode. set orthoscopic ray is the workaround. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San

[PyMOL] EMizing an xray structure

Hey all, I'm trying to make a figure from a pdb that's supposed to look like an EM structure. According to an older post from Warren I should increase solvent_radius and alter vdw. For most combinations of the two, artefacts appear all over the place, like missing surface and surface

Re: [PyMOL] EMizing an xray structure

You can create an mrc map from a PDB using the pdb2mrc program in the EMan package (http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/ and http://ncmi.bcm.tmc.edu/homes/stevel/EMAN/doc/progs/pdb2mrc.html). Pdb2mrc allows you to specify parameters that would affect what a theoretical cryo EM 3D

RE: [PyMOL] EMizing an xray structure

Try a command sequence like this: alter all,b=10 set gaussian_resolution, 9.0 map_new dcalc, gaussian, 3.0 map_double dcalc isosurface dsurf, dcalc, 1.0 Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite