[Chimera-users] Presets and multiple structures
meng at cgl.ucsf.edu
Tue Oct 14 12:49:48 PDT 2008
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.
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
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
preset apply int 1
(** 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.
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