[Chimera-users] Presets and multiple structures

[James Nettles]

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%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 at 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 at 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)
________________________________________________________




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