[Chimera-users] Show backbone chain-trace by default

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 9 16:05:28 PDT 2013

Hi Thomas,
Not exactly.  There are some options as to how structures are initially displayed in the Preferences, category: New Molecules, but they are far from comprehensive.  The choices are basically the default ("smart initial display") with atomic detail for small molecules and binding sites and ribbons for biopolymers, or all atoms.

I would recommend figuring out the commands that give you exactly what you want and then using alias.  Then it would just be one step after opening the molecule instead of multiple (hiding ribbon, showing backbone trace, etc.).  It depends what you want, but maybe something like command:

alias ^trace ~ribbon; show @ca

... which will make a top-level Aliases menu with "trace" in it, and you could execute the alias by choosing that from the menu or entering it in the command line.  If you wanted to keep the atomic detail of binding sites as in the default initial display, you would use "display" or "disp" instead of "show" in the example.  You could append additional commands with semicolons within the alias.  More about alias here:

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 Aug 9, 2013, at 2:05 PM, Thomas Hrabe wrote:

> Hi everyone,
> I was looking for the setting to tell Chimera to open a PDB file in backbone chain-trace mode rather than looking at the ribbon.
> Is that possible?
> Thanks in advance,
> Thomas

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