RE: [PyMOL] secondary structure

[DeLano, W. <wa...@su...>]

> How does this affect movies involving conformation changes?  Secondary
> structure info from the first frame appears to carry over=20
> into the others-
> whereas in reality some helixes or sheets change to varying=20
> degrees.  This
> leads to warping in something like calmodulin.  Would I need to render
> frames separately and run 'alter'?

Secondary structure in PyMOL is currently an atomic not a coordinate
property.  This is probably a design flaw, which will need to be fixed
later on.  Same goes for occupancy and B-factors (anything else?).

Anyway, if you want it to change secondary structure during a
trajectory, the easiest thing to do is split the trajectory over two
objects with non-overlapping states (ie. use the 'state' option to
load), and then assign the secondary structure independently...

state    1 2 3 4 5 6 7 8 =20
object1  X X X X=20
object2          X X X X=20

> However, I'm finding that using PyMOL as a module is failing. I built
> from source and have everything installed in=20
> /usr/local/python, and when I
> try to do 'from pymol import cmd, util' I get this:
> Traceback (most recent call last):
>   File "./render.py", line 7, in ?
>     import pymol
>   File "/usr/local/pymol/modules/pymol/__init__.py", line 24, in ?
>     import _cmd
> ImportError: shared object not open

The easiest way to use PyMOL as a module is to use PyMOL as your Python
interpreter.  It isn't trivial to launch PyMOL from within a running
Python interpreter, but it can be done under unix (only).  See pymol.com
and modules/launch_pymol.py for an example of how to do it.