Thanks for the idea Warren! I'd actually be more than happy to get my
hands dirty in the actual code but I wasn't able to figure out how to
change coords. I tried changing the coords in the chempy atoms e.g.
for a in cmd.get_model("myprot").atoms[:1]:
print a.coords
a.coords[0] += 1
print a.coords
for a in cmd.get_model("myprot").atoms[:1]:
print a.coords
a.coords[0] += 1
print a.coords
[0.37400001287460327, 0.37400001287460327, -0.95200002193450928]
[1.3740000128746033, 0.37400001287460327, -0.95200002193450928]
[0.37400001287460327, 0.37400001287460327, -0.95200002193450928]
[1.3740000128746033, 0.37400001287460327, -0.95200002193450928]
but the changes don't seem to stick. Is there some other way via the
python API?
Thanks!
-Will Sheffler
Baker Lab
University of Washington
On Mar 28, 2007, at 6:45 AM, DeLano Scientific wrote:
Will,
The easiest approach, short of Python programming, is to
temporarily load a
new pdb file with updated coordinates and simply update the
existing object
before deleting the original.
load original.pdb
unset auto_zoom
# then repeat the following as often as necessary
set suspend_updates
load updated.pdb
update original,updated
delete updated
unset suspend_updates
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:del...@delsci.info
I'm interested prototyping some interactive molecular modeling and
simulation code using pymol. I know one can change the atomic
coordinates
wholesale in simple ways via alter_state (like x=x+1). Is there an
efficient
way to change all coordinates to arbitrary values (like coordinates
output
from a simulation)? I could select each atom and alter_state it's xyz
values, but I'm hoping there is a better way.
Thanks!
-Will Sheffler
Baker Lab
University of Washington
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