> How does this affect movies involving conformation changes? Secondary > structure info from the first frame appears to carry over > into the others- > whereas in reality some helixes or sheets change to varying > 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 object1 X X X X object2 X X X X > However, I'm finding that using PyMOL as a module is failing. I built > from source and have everything installed in > /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.
