[Chimera-users] color by height

p.j.depablo p.j.depablo at gmail.com
Fri Jul 5 00:30:32 PDT 2013

Thank You Elaine. It helped a lot!

On Thu, Jul 4, 2013 at 6:37 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Pedro,
> I guess you are using the "Surface Color" tool, in which the "axis" field
> refers to the data's own coordinate system.  However, the "scolor" command
> allows using the coordinate system of a different model than the data,
> which will let you do what you want.
> Unfortunately it is a bit tricky, especially if you spent a lot of time
> generating the current positions of your models (structures and maps) and
> don't want to do all that again.
> First, the slightly simpler case in which you don't mind repositioning all
> your models again. Steps:
> (1) reset everything to its original untransformed position, losing the
> current positions (command: reset). DO NOT MOVE ANYTHING.
> (2) open some reference model; it doesn't matter what, since it will be
> hidden, so might as well choose something simple and small.  DO NOT MOVE
> (3) show Model Panel (under Favorites menu) and in that tool, both
> deactivate and hide the reference model (un-check "A"ctive and "S"hown for
> that model).  Deactivating means it is frozen in place, and since you never
> moved it since resetting everything to default, its coordinate system will
> match the "laboratory" (display) coordinate system where X is horizontal, Y
> vertical, and Z in/out of screen.
> (4) re-position the other models as you like
> (5) use the scolor command referring to the hidden reference model's
> coordinate system.  For example, if your displayed surface is #0 and the
> hidden reference model is #2:
> scolor #0 geometry height axis y cmap rainbow coord #2
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html>
> At first I thought it would work to save the position of all the original
> models (command: savepos position_name) before opening the reference model,
> then restoring the position (command: reset position_name) before coloring,
> but that does not work because it will move the reference model along with
> the other models.
> The only way I could think of to avoid regenerating the positions of all
> your models is to save transformations to a matrix file and then manually
> text-edit the file to un-transform the reference model:
> (1) don't worry about resetting anything... with all the models in their
> desired positions, just open the reference model and then save all matrices
> to a file with command "matrixget matrix-filename" (you can also specify
> file location as the path before the filename)
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/matrixset.html>
> (2) in text editor, edit the transformation matrix of the reference model
> to no transformation, for example:
> Model 2.0
>         1 0 0 0
>         0 1 0 0
>         0 0 1 0
> (3) apply the resulting set of matrices back onto your models with command
> "matrixset matrix-filename" (again you can include path); only the
> reference model should move
> (4) hide and deactivate the reference model with Model Panel as above
> (5) use scolor as above
> I tried both approaches just now to make sure they work as described.
>  Sorry there are so many steps.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jul 4, 2013, at 7:34 AM, p.j.depablo wrote:
> > Hi everybody
> > I am interested in coloring an EM volume by height. In this option you
> can change the origin and the axis of coloring. Specifically, I rotate t
> the structure untill a  desired orientation. Then, I would like to choose
> the axis of coloring to be the same as the view axis, but can not find the
> viewing axis coordinates. Is there possible to find this informaton
> anywhere?
> > Thank you in adavance.
> > Pedro
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