[Chimera-users] View scale and brix output

Tom Goddard goddard at cgl.ucsf.edu
Wed Mar 7 09:49:09 PST 2007

Hi Christopher,

  If I understand your request you want to be able to easily return to a 
standard view magnification for making figures.

  There are 3 parameters that determine the apparent size of models seen 
in the Chimera window: the distance of the models from the eye position, 
the angular field of view, and the scale parameter which relates the 
screen pixels to physical units (Angstroms).  With orthographic 
projection only the scale parameter matters.  Chimera can use 
orthographic projection (activated in Camera tab of Side View dialog) 
but the default is perspective projection where all 3 parameters 
matter.  Assuming you don't change the distance between the eye (i.e. 
camera) and the models, and you don't change the field of view then 
setting the scale alone would be sufficient to return to standard 
magnification settings.

  In the Side View dialog (menu entry Favorites / Side View) under the 
Camera tab there is an entry field for the scale factor.  It gives the 
current absolute scale factor and can be changed to whatever value you 
like.  It starts out as 1.0 in a new Chimera session.  But if you open a 
session file it is set to whatever it was in the original session.

   If you open a session for a figure, then modify it, changing the 
scale as you go, then want to return to the original session scale 
factor you could use the command "reset session-start".  This not only 
resets the scale but also the positions and orientations of all the 
models.  Maybe that is not what you want because the new figure is 
perhaps showing the models from a different direction (e.g. rotated by 
90 degrees).  So perhaps you need a command like "resetscale 
session-start".  That resetscale command does not exist but I could 
probably add it if you think it is what you need.

  Regarding writing BRIX map files, I agree it would be handy if Chimera 
could output more map formats.  I think BRIX format is well enough 
documented that it could be done (writing files requires better 
understanding of the format than reading them).  That format only saves 
unsigned 8-bit data values though.  So going from float values in MRC to 
BRIX will lose information.  Maybe Chimera would issue a warning about that.


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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