[PyMOL] movies and secondary structure

Hi all,

I would like to make a movie from a trajectory of 50 frames with varying
sec structure. Following Warren's advice in a previous thread (see below)
I load every pdb file into a different object *and* state using
  file_list1 = glob("*_first.pdb")
  for file in file_list1:
     cmd.load(file,file,file[:1])

{ files are named 1_first.pdb, 2_first.pdb ...}
However, the object loaded to the first frame also appears in the
following ones. dssp calculation with rtools just gives the sec structure
of the object in the first frame.
As a workaround I tried to start loading into the 2nd frame and not to
load anything into the first one. But then the command "dssp
(2_first.pdb)" gives an error "no atoms selected" instead of any calculation.

Any suggestions?
Frauke


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RE: [PyMOL] secondary structure

    * From: "DeLano, Warren" <wa...@RE...>
    * Date: Wed, 13 Feb 2002 13:43:10 -0800
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    * Thread-topic: [PyMOL] secondary structure

> 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