[Chimera-users] Presets and multiple structures

James Nettles jnettle at emory.edu
Thu Oct 16 12:00:10 PDT 2008

Thanks to you both.

The excellent functionality of Chimera is only surpassed by the  
extraordinary support you give your users.

We REALLY appreciate it!


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
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>> Chimera-users at cgl.ucsf.edu
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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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