Re: [PyMOL] a scaling question

[Robert Campbell]

Hi Fei,

* Fei Xu f...@rutchem.rutgers.edu [2006-04-19 11:55] wrote:
 Hi!:
 I met a scaling problem.
 I created many pdb files along one trajectory of DNA movement. I loaded
 each pdb file in pymol to create a picture, that is, one frame of the
 trajectory. Pymol shows each molecule in an optimal size automatically
 according the general shape of the molecular. The shape of the molecule
 along trajectory kept changing so that the size of the molecule also kept
 changing. When I connected all the time frames together, I saw the funny
 effect that the molecule was jumping back and forth.
 How can I put the molecule in the different time frames in exactly the
 same size?

What you are experiencing is the auto_zoom feature of pymol.  I have
this turned off in my .pymolrc file.  You can type:

  set auto_zoom, 0

to disable this feature.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D. r...@post.queensu.ca
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6  Canada   http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] a scaling question

[Peter Adrian Meyer]

Fei,

The easiest way would be to use get_view/set_view.
1. Move your first frame pdb around until you're happy with the view
2. type get_view (pymol viewer window, or pymol gui window), and save the
output in a new text file (I'd call it view.pml, but that's just me)
3. Load all of your frames in a script (which you're probably doing
already), change load frame2.pdb to load frame2.pdb ; @view.pml for all
of your frames (or change whatever loop structure you're using).

This way all of your frames will be in the same scale, as well as
orientation (which may not be what you're looking for).  If you only want
to control scale (not orientation), then you could probably work something
up that only takes the scale parameters out of the orientation matrix.

Hope this helps,

Pete

 Hi!:
 I met a scaling problem.
 I created many pdb files along one trajectory of DNA movement. I loaded
each pdb file in pymol to create a picture, that is, one frame of the
trajectory. Pymol shows each molecule in an optimal size automatically
according the general shape of the molecular. The shape of the molecule
along trajectory kept changing so that the size of the molecule also
kept
 changing. When I connected all the time frames together, I saw the funny
effect that the molecule was jumping back and forth.
 How can I put the molecule in the different time frames in exactly the
same size?
 Thanks!
 Fei





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Pete Meyer
Fu Lab
BMCB grad student
Cornell University