Dear all,
The size of isotropic atoms plotted by using "alter all, vdw =
sqrt(b/8)/pi" and "show sphere" looks small compared with the size of
anisotropic atoms displayed by "show ellipsoid" in PyMOL default setting
with 50% probability.
How can I plot the isotropic atoms with 50% probability?
T
thank you very much, Ali!
I only changed the quotes in your script because I have integrated it
to my shell script in order to use with the varibables:
# run pymol to align the snapshots and save it to the session
pymol -c -d "
from pymol import cmd
cmd.load('${sim}/${simulation}_after_min
Hi James,
Just a follow up, I would still recommend you use the script in a file to do
this as it is less messy but it can be done:
pymol -c -d '
from pymol import cmd
cmd.load("A.pdb")
cmd.load("B.pdb")
cmd.load("C.pdb")
cmd.super("C*","A*")
cmd.super("B*","A*")
cmd.bg_color("white")
cmd.save("
hello there,
As a part of my scripting routine, I would like to use pymol in no-gui
mode (directly in the linux shell) to do the following things:
1) load in pymol 3 conformations of the same protein, which are
defined as A.pdb B.pdb C.pdb
2) superimpose C to A using "super" or alternatively (whic
