[Chimera-users] Using Chimera to read Maestro files

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 30 14:02:17 PDT 2015

Hello Chris Deer,
Chimera reads the molecular structure data from Maestro files, but not display settings such as coloring and styles.

Currently, you would have to set colors and display styles “manually” in Chimera to try to reproduce the appearance in Maestro, sorry.  From squinting at your Maestro image, maybe something like Chimera commands:

show protein
repr wire
linewidth 2
color red :.A
color sky blue :.B
color white :.C
color orange :.D
ribinside dim gray
color byelement
~set depthcue

You would have to figure out which chain is which to reproduce the desired coloring.  The command “back solid white” would give a white background. Not so bad if you only have a couple of Maestro files, but impractical for high-throughput processing.

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 Jun 30, 2015, at 7:56 AM, CG Deer <deernet at gmail.com> wrote:
> Hello Chimera Developers and Users,
> My name is Christopher Deer, and I am trying to use Chimera as part of a workflow for getting a maestro file (.mae) ready for presentation in a CAVE environment.  The .mae file contains color references and specifics defined by a researcher.  However, these details are not appearing when I open the file in Chimera.  So is there any way to open this file type without having to redefine all the specific features the researcher originally made?  
> Here is a screenshot of what I am seeing in Chimera, and I have attached what the researcher originally wanted it to look like (minus white background).<image.png>
> Thank you for your help,
> --Chris Deer
> University of Arizona Research Computing,
> Data Visualization Specialist
> <exo_complex_may.png>

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