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%20Molec...

see also the "New Surfaces" category: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfa...

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

Thanks to you both. The excellent functionality of Chimera is only surpassed by the extraordinary support you give your users. We REALLY appreciate it! Jim On Oct 14, 2008, at 4:06 PM, Eric Pettersen wrote:

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%20Molec...

...

see also the "New Surfaces" category: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Surfa...

...

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

________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine Laboratory of Biochemical Pharmacology (LOBP) Computer Assisted Discovery Research Environment (CADRE) ________________________________________________________