[Chimera-users] on movie command

Elaine Meng meng at cgl.ucsf.edu
Sun Oct 18 10:02:02 PDT 2015

Dear Smith,
I would first create and save the positions (command “savepos” including the position name) and save them in a session along with the protein.  Then,  you could re-open the session later several different times to work on creating the movie script and/or doing the recording, without having to re-make the positions each time.  For the movie, you could restore positions smoothly using “reset” including the position name, or maybe even “fly” for restoring multiple positions one after the other.

The hard part is creating the positions.  If you are willing to do it interactively (manually), moving the protein by hand to find each position before using “savepos,” that will probably give the most attractive results.

Generating positions automatically is less tedious but much less effective, because there will usually be problems like something blocking the view of something else.

The following examples are for residues 10-20 in model 0 chain A. It is easy to use window or focus, but note they will change the scale (zoom) and clipping planes, and will not do any rotation, so that the residues might on top of each other.

window #0:10-20.A
(- or -)
focus #0:10-20.A

If you really want to avoid changing the scale, but allowing rotation is OK, you could try using align to stack the residues along Z followed by a 90-degree rotation to stack them along X instead of Z:

clip off
align #0:10-15.A #0:16-20.A
turn y 90

See the documentation for details/options of the various  commands.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 18, 2015, at 7:10 AM, Smith Liu <smith_liu123 at 163.com> wrote:

> Dear All,
> Suppose there is a 100-residue protein opened in chimera, and it was scaled to a windows which can hold 10 residues, for example residue 10-20. Is any good way we first center on residue 15, then smoothly center on residue 16 (window hold residue 11-21), then smoothly center on residue 17 (window hold residue 12-22),  then smoothly center on residue 18 (window hold residue 13-23), ......., until we center on residue 100? Here I emphasize "smoothly" so that the residue "move" was not too sudden to the eye.
> Best regards.
> Smith

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