[Chimera-users] Presets and multiple structures

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 14 12:49:48 PDT 2008

Hi Jim,
Presets always act on everything; they include global settings (e.g.  
background color) and adjust depending on what structures are present  
(different results for one chain vs. multiple chains in one model vs.  
multiple models).

However, presets are just multiple steps rolled into one for your  
convenience.  You can perform the desired steps on models selectively  
using the Actions menu and/or commands.  If you first select the  
model, the Actions menu items will apply only to that model: hiding  
atoms, showing ribbon, changing ribbon style to smooth, etc.  With  
commands, you can specify what you want to do (verb) and what you want  
to do it to (subject) all in one.  The descriptions of the presets  
will give you some information on what they comprise, but feel free to  
write back if you have trouble identifying the needed menu item or  

A related feature you might not know about is the "New Molecules"  
category within Preferences (Favorites... Preferences).  You can  
specify how you want structures to appear when first opened (remember  
to click Save if you want settings to apply to later uses of  
Chimera).  This panel is not complete, however... for example, there  
is no option to undisplay the atoms.
see also the "New Surfaces" category:

Yet another possibility is to make a command alias that does all your  
favorite things,

For example, start chimera, show the Command Line (Favorites...  
Command Line) and try the commands:

alias makenice ~disp $1; ribbon $1; ribrep smooth $1; col byhet $1;  
rep stick $1; disp $1 & ligand z<4
open 2gbp
open 1zik
preset apply int 1
open 2mnr
makenice #2

(** that alias command should be all one line even though the annoying  
mail program will probably insert a return **)

That opens 2gbp as model #0, 1zik as #1, and 2mnr as #2.  Since #2 was  
opened after the preset was used, it can be adjusted without affecting  
the other models by way of the alias "makenice".

Aliases are saved in sessions.  You could even make a command file  
with that alias command in it and simply open the command file in  
different Chimera sessions to create the alias.

In the Model Panel, "active" means movable, such as with the mouse or  
movement commands such as "move":

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 14, 2008, at 11:07 AM, James Nettles wrote:

> Something that often comes up is that I have some number of aligned  
> protein structures with nicely color coded  secondary features and  
> specific side chains. I then want to fit another molecule in this  
> same space and apply a "preset" graphic mode to the new structure  
> without undoing the previous molecular views.
> I expect this is possible, but I haven't gotten it to work yet. I've  
> tried making only my molecule of interest "active" in the Model  
> Panel, but  the preset still effects everything.
> I'm using Alpha build 2557 2008/09/13 at the moment.
> Thanks,
> Jim

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