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

Xing Zhang xzhang1999 at ucla.edu
Tue Feb 7 14:20:51 PST 2012

Hi, Elaine,

That's very helpful. Thanks much.


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Tuesday, February 07, 2012 11:39 AM
To: Xing Zhang
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] how to setup a default settings for a new pdb

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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