Try something like this:
# Save as a .pml file
load $PYMOL_PATH/test/dat/pept.pdb
for st in range(2,31): \
cmd.create("pept","pept",st-1,st) \
cmd.frame(st) \
cmd.edit("4/cb","4/ca") \
cmd.torsion(5)
edit
movie.sweep
rewind
mplay
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Hi,
I'm trying to create a simple movie showing the rotation around a
dihedral angle. I'm sure it's an extremely easy task, but I can't figure
out the way of loading each state (i.e. conformation of the dihedral
angle) into the movie object. I mean, the 'load' command (as in "load
foo1.pdb,mo
I agree with the Logitech sentiment. I have a MX 700 for my iMac,
and installing the software was a bad idea when I had Panther. I
haven't tried installing it on Tiger, but all the buttons (8 of them)
are assignable in the System preferences menu. In addition, it's
cordless, and the batt
Hello Warren,
Thanks for the response.
That is exactly what I have done--taken structures produced with
builder and brought them into GROMACS and have obtained minimized
structures, but as Jim Nettles mentioned, such techniques can depend
on what the initial structure is, so I was just won
James,
PyMOL's peptide & small molecular builder is no more rigorous that a
handheld plastic model. Unfortunately, DeLano Scientific doesn't have
the developer "bandwidth" right now to get into the simulations
business. Instead, we hope to facilitate and encourage integration with
existing exter
I have one of each of the Logitech MX 500, 510, 518 series and they
all have worked (and are still working) fine for me, albeit on windows
and linux. I don't have any experience with the cordless version, but
after a little google searching it looks like the logitech software is
buggy on macs. Yo
Hello James,
There is really a lot of room for discussion regarding your questions.
Considering peptide conformations is complicated business and there is
generally not "a" structure. There is great conformational flexibility
even for small, constrained, cyclic peptides. As for the MD - yes,
Hello All,
How "physiological" are the structures that are produced from
builder? Meaning, how are the angles, etc. determined? Might such a
resulting structure mimic a chemically-synthesized peptide?
I have taken peptides I created using builder and done some MD
simulations and the struc
Quoting tanri...@stud.uni-frankfurt.de:
# Hi everybody,
#
# i've just created many CGOs, which show up solid surfaces like spheres
and
# ellipsoids. Is it possible to set the transparency of some CGO's to
i.e. 0.5
# and leave the others solid?
# I've checked out the reference and the manual, an
Lari,
the way you've described is a nice workaround for images and presentations,
which I had in mind, too. But it is not applicable while I am working with
PyMOL online and want to make my CGO's transparent to see what is in them
(including ability to rotate and zomm in/out the scene (which is n
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