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
--------
RE: [PyMOL] secondary structure
* From: "DeLano, Warren" <[email protected]>
* Date: Wed, 13 Feb 2002 13:43:10 -0800
* List-archive:
<http://www.geocrawler.com/redir-sf.php3?list=pymol-users>
* List-id: PyMOL Users Group <pymol-users.lists.sourceforge.net>
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* Thread-index: AcG0WofecTamzeK5QwiLfKAn/1zEHgAe2fOQ
* 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
