Hi John,

  In ChimeraX you can use command "zoom pixelSize 5" to make the view 5 Angstroms per pixel.  This is at a depth into the screen that matches the center of rotation since it is using perspective projection so things further away appear smaller.  You could use "camera ortho" to get orthographic projection where the pixel size will be the same at all depths.

  You are using our older program Chimera.  You might want to use ChimeraX for figures because it provides better shadowed lighting which shows depth.  Here's a comparison of ChimeraX style soft lighting on the left and Chimera lighting on the right.

  If you have Chimera session files, ChimeraX does not read those.

  Tom

soft lightingsimple lighting



On Nov 19, 2019, at 8:02 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:


On Nov 19, 2019, at 5:56 AM, JOHN FLANAGAN <jmf27@psu.edu> wrote:

Hi
 I am trying to compare several negative stain em maps to make a figure.  For what I want to do its easier not to have all of the maps loaded at the same time.  However, I am having trouble keeping everything on the same scale.  I am able to set the windowsize, center the maps but the zoom is not always the same.  I searched the web and found that there used to be zoom and setzoom commands that should do the trick, but neither is recognized in my version of chimera (commands I mean).  All of the maps have the same starting A/px but what I want to do is take the map with the largest extent and set that and whatever its being aligned too to fill the window then for every other session have the same windowsize and effective zoom.  Pardon my inelegant description but I hope that provides sufficient explanation for what I am trying to do.

Cheers
John

Hi John,
Sending this to chimera-users@cgl.ucsf.edu, the recommended address for Chimera questions.  That way, whoever has the expertise can answer, and others can benefit.

This previous post may answer your question.  It says you have to download the setzoom command code separately and provides a link.
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2017-January/013091.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




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