[Chimera-users] how to setup a default settings for a new pdb model?

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 7 11:39:25 PST 2012

Hi Xing,
First figure out the series of Chimera commands that do what you want, then make it an alias.  You can have several aliases.  For example, command (all one line, the mail program may break it up):

alias ^mypreset ~ribbon; show @n,ca,c,o; repr stick; setattr m stickScale 0.5; color byatom; color green C

will put "mypreset" in an "Aliases" menu.  Choosing that menu item will affect all the models at once.  To only affect a specified model, you can also make aliases with arguments, for example:

alias ^mine2 repr bs $1; color red $1

In that case it would not appear in the menu, but you could use it in the command line, for example to apply it to model #5:

mine2 #5

All aliases are saved in sessions, but only the aliases that go into the menu are saved in your preferences file.  If you want to have the argument-type aliases automatically available, you could instead put the alias commands in a Chimera command file (plain text) and then specify that as a startup file in the Preferences (Favorites... Preferences in the menu), category: Command Line.  These files are automatically executed as soon as you show the Command Line.

More details on the alias command:

The drawback is that you would need to figure out the Chimera commands for your desired settings.

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 Feb 7, 2012, at 11:15 AM, Xing Zhang wrote:

> Hi,
> I have many different pdb models that need to be displayed at exactly the same settings, including color, background, stick scale and so on, so I want to set all these settings for the first model, and then apply these settings to a newly opened pdb model. Is there any way to save and load a default setting for a new pdb model?
> Thanks much.
> Xing

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