Re: [PyMOL] surfaces for molecules with non-standard VDW's

solvent_radius,3 That seems to do the trick for me. Cheers, Tsjerk On 5/22/07, Richard Gillilan wrote: In the past I have used PyMol pretty successfully to visualize low- resolution x-ray solution scattering results in which each "atom" in a pdb file is actually a large spher

[PyMOL] surfaces for molecules with non-standard VDW's

In the past I have used PyMol pretty successfully to visualize low- resolution x-ray solution scattering results in which each "atom" in a pdb file is actually a large sphere (say 4-6 Angstroms) representing some density. I would use >alter , vdw = 6.0 to set the sphere sizes appropriate

Re: [PyMOL] simple cgo question

Thanks Rob, that worked! Load it into PyMOL with: PyMOL> run arrows.py

[PyMOL] simple cgo question

I'm probably making a simpler mistake here, or perhaps there is something wrong with my installation or paths. I'm trying to load and display the simple cgo example in the manual. I created a file named "arrows" containing this definition: from pymol.cgo import *# get constants from pym

[PyMOL] dock one protein into another?

I'm having trouble figuring out how to use the edit mode in PyMol. I would like to dock an entire protein (a homodimer along with water) into another structure by rotating and translating manually. Is there a way to move multiple molecules like this as a group? Thanks Richard Gil

[PyMOL] surfaces, VDW and probe radii

I'm trying to create a smooth surface representation of a set of 6.5A diameter spheres read in as CA atoms. Is there a way to override PyMol's assignment of atomic radii? Also, if I were using a conventional molecular surface algorithm I would turn up the "probe" radius so that the surface

[PyMOL] Depth buffer and close surfaces

very narrow, but messy surface intersections persist. I could touch up the image with GIMP, but does anyone have a clever solution to this problem? Richard Gillilan MacCHESS Cornell

[PyMOL] Re: [ccp4bb]: Pymol stereo question

On Wednesday, June 4, 2003, at 07:53 PM, Tim F wrote: The fact that points on the object that are very close to the viewer or very far away appear double (and out of focus) is also exactly what happens with real vision. Here's an experiment to try: True, but you're describing horizontal (d

[PyMOL] Re: [ccp4bb]: Pymol stereo question

lso be sure to check out Richard Gillilan MacCHESS, Cornell This method of generating stereo images is correct, but also leads to quite a bit of vertical parallax (the so-called "toe-in" projection) - this is why many stereoscopic images are hard to view properly (usually, edges

[Fwd: [PyMOL] Apple new version X11]

Richard Gillilan wrote: Sorry, intended this to go out to the whole group. Here goes again: > > Craig Smith wrote: > > > > I've installed X11 server through XDarwin. Will the installation of > > PyMOL for OS X described on your web page work with XDarwin's

Re: [MMTK] Re: [PyMOL] improving interoperability between python moleculetoolkits (fwd)

> Konrad Hinsen wrote: > > Indeed. But this illustrates nicely a frequent problem faced by > software designers: Software like OpenDX is powerful and flexible, but > also huge and difficult to learn. A small specialized tool is easier > to use for the specialized user. Of course those users then f

Re: [PyMOL] improving interoperability between python moleculetoolkits

macromolecule groups (Michel Sanner of Scripps gave a nice talk on his Python-based modeling system). Worth looking into. Richard Gillilan MacCHESS, Cornell

Re [PyMOL] Re: mice for OSX PyMOL

On Monday, September 9, 2002, at 06:33 PM, Luca Jovine wrote: I use a basic Logitech 2 button + wheel mouse, and it seems to work just fine... -Luca I have the same mouse and love it. I've always thought it would be really nice if you could rotate models using the wheel. (Perhaps PyMol alre

Re: [PyMOL] Mac OS X install, general PyMOL function - badly need overview

(http://developer.apple.com/technotes/tn2002/tn2053.html). Richard Gillilan MacCHESS, Cornell

Re: [PyMOL] Babel and File Format Conversion

objects. http://openbabel.sourceforge.net Richard Gillilan MacCHESS, Cornell Bob Havlin wrote: > > Great software! You have done a wonderful job. > > You probably know about this already, but incorporating the file format > converter > named babel > > http://www.eyesopen.com/bab

[PyMOL] Beamtime at Cornell

last. PyMol is available at our facility. Thanks Richard Gillilan MacCHESS Cornell -- Protein Crystallography at MacCHESS -- MacCHESS, the macromolecular structure facility at the Cornell High-Energy Synchrotron Source, offers high-brightness x-ray beamtime to ge

Re: [PyMOL] About Surface

would be happy to send you a copy of the code. Sorry I have not time to work with PyMol yet, perhaps someday. Richard Gillilan MacCHESS "DeLano, Warren" wrote: > Now, on to Alan's specific questions: > > > I'm particularly interested in how pymol generate