[Chimera-users] Custom presets

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 6 14:24:54 PDT 2007

Hi Eric,
Easy question first... I can think of three ways to turn off halfbond  

- open the Model Panel (under Favorites), choose the models of  
interest in the left side, choose "attributes" on the right.  In the  
model attributes panel, expand the "Component Bond Attributes"  
section, turn "halfbond mode" to "off"
- select one or more bonds of interest, click the button on the lower  
right corner of the Chimera window that says what it selected (opens  
the Selection Inspector).  In the Selection Inspector, go the bond  
section if you aren't there already, turn "halfbond mode" to "off"
- use the command "bondcolor" (which also specifies a particular  
color for the bond)

The Presets are pretty new, and currently there is no friendly way  
(without Python programming) to make your own presets. We plan to add  
this in the future.  There is also no friendly way to transfer one  
molecule's attribute settings to another.

However, there are some related things that may help:

- the Preferences include a New Molecules section in which you can  
specify some display attributes of newly opened molecules.  However,  
the options are not complete, i.e. not all attributes you might want  
are controllable there.

- if you have a series of commands that set the attributes, you can  
save them to a command file (or create a command file from scratch in  
a text editor).  Opening the command file will execute all the commands.

- you can alias a long command or multiple semicolon-separated  
commands to a short string that is much easier to type.

If you have specific suggestions or ideas, don't hesitate to share  
more information about your situation.  We can factor them in to our  
plans.  I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 6, 2007, at 10:21 AM, Eric Ganz wrote:

> Is there a way to create new presets for molecule views?
> We want to apply the attributes of one molecule to subsequent  
> molecules.  Is
> there an easy way to do this?
> Our second question is how to set half-bond mode off for our views.

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