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 find
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
implementation of X11 or do I have
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 of the image are out of focus). What
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
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
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 Gillilan
Thanks Rob, that worked!
Load it into PyMOL with:
PyMOL run arrows.py
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 molecule name, vdw = 6.0
to set the sphere sizes
