[Chimera-users] View scale and brix output

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 7 12:06:39 PST 2007

Hi Christopher,
Tom did mention "reset," but I thought I'd expand on that topic a bit.   
You can actually save multiple named positions, which will then be  
included in a single saved session.  When I make a set of figures that  
differ in view and scale but with basically the same display/coloring  
setup, I use the "savepos" command to save the position for each  
figure, and then save the session.  It doesn't matter what position  
everything is in when you save the session, because you will still be  
able to get back to any of those saved positions with "reset."

The saved positions include scale.  If you really only want to restore  
scale, currently you could note the value shown in the Camera tool (as  
mentioned by Tom), and later type that into the Camera tool to restore  

more about savepos and reset:

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

Christopher Akey wrote:
> Tom-
> A few more issues that have come up for user friendliness.
> 1. It would be useful to have a box where the user can specify the
> absolute scale for the session, the first time it is opened, this
> could be set at 1.0 for example after loading a ribosome map and the
> atomics and putting them to a good size.
> Then the program should keep track of the changes made during the
> session using the scale command (I guess you can't track changes made
> with the mouse so one generally would avoid this, or even better one
> should be able to turn off the mouse scale feature!).
> This way one could always look at the pull down for the current scale
> value when you capture a particular view for a figure.
> One could then return to the original scale of 1.0 at the end of
> session or write down the current scale value, which could be kept in
> the ssesion. So upon reopening the session at a later date, one can
> always get back to the correct scale to recapture a panel for a
> figure. This is currently a real problem, as far as I can tell.
> 2. We often want to import a brix file with aligned pdbs, since we
> dock and look at them in 'O', which is better in some ways for looking
> at these maps, but not so good as Chimera for figure making
> obviously....then in Chimera we may continue to trim or segment a map,
> and then we want to take it back out, presumably as an MRC file, to be
> converted into a brix by a conversion program (for us its SPIDER).
> Then one can do another cycle of docking in 'O' using the
> refined/cleaned up sub map from Chimera.
> While I can think of one way to do this without losing the relative
> origins and thus, the map alignments, it is pretty tedious. If one
> could write the zoned or volume erased brix volume back out as a new
> brix file, with the correct dimensions and origin, relative to the
> brix file brought into Chimera, this would allow you to cycle back and
> forth using the best of both programs.
> cheers  C Akey

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