On top of Elaine's good suggestions, there's a horrible kludge that you could possibly use.  Before you open your additional structure, save a session.  Then open your new structure, position it, and close the other models.  Apply your preset.  Restore the session you saved and when Chimera asks you if you want to close existing models say no.

--Eric

On Oct 14, 2008, at 12:49 PM, Elaine Meng wrote:

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

command.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets>

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.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules

see also the "New Surfaces" category:

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfaces

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

favorite things,

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html>

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.

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile

In the Model Panel, "active" means movable, such as with the mouse or

movement commands such as "move":

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>

I hope this helps,

Elaine

-----

Elaine C. Meng, Ph.D.                          meng@cgl.ucsf.edu

UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab

Department of Pharmaceutical Chemistry

University of California, San Francisco

                    http://www.cgl.ucsf.edu/home/meng/index.html

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

_______________________________________________

Chimera-users mailing list

Chimera-users@cgl.ucsf.edu

http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users