[Chimera-users] modifying presets

[glenn millhauser]

Thanks, Elaine.  This helps get me started.  I will play around a bit  
with a command file.  I bet it will come together easily.
all the best,
glenn


On Feb 20, 2008, at 3:55 PM, Elaine Meng wrote:

> Hi Glenn,
> Although we plan to have user-defined presets in the future,  
> currently there is no reasonably user-friendly way to customize them.
>
> As a stopgap, if there are a few commands that generate the display  
> you want (and you could start with a preset command), you could:
>
> - put them in a command file; simply opening the command file in  
> Chimera would execute it
>
> - alias some word like "mypreset1" to those commands all strung  
> together with semicolons, then later you would only have to type the  
> command "mypreset1"
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html
>
> You can have a command file automatically read at Chimera startup.  
> This is specified in the preferences:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Midas
>
> You would only put the alias commands there, not the display  
> commands themselves, since you want to control when those commands  
> are executed (and usually at startup no structures have been opened  
> yet anyway).
>
> There is also a New Molecules section of the preferences in which  
> you can control how structures are displayed when they are first  
> opened:
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules
>
> However, the New Molecules options are rather limited compared to  
> what you can do with commands.  There is nothing about disulfide  
> bonds, for example.
>
> I would be happy to provide more detailed help with any of this if  
> you would like.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                     http://www.cgl.ucsf.edu/home/meng/index.html
>
>
>
>
> On Feb 20, 2008, at 3:31 PM, glenn millhauser wrote:
>
>> Hi Folks,
>>   Is there a way to edit the Presets to include additional protein  
>> features?  Specifically, I work with quite a few disulfide rich  
>> proteins and it would be great to select the Preset Interactive 1  
>> and have it automatically draw Cys side chains with disulfide links.
>> Many thanks,
>> glenn
>>
>>
>> Glenn L. Millhauser
>> Department of Chemistry & Biochemistry
>> UC Santa Cruz
>> Santa Cruz, CA 95064
>> 831 459 2176 voice
>> 831 566 3337 cell
>> 831 459 2935 fax
>>
>> http://chemistry.ucsc.edu/~glennm
>> http://www.chemistry.ucsc.edu/faculty/millhauser.html
>>
>>
>> _______________________________________________
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>



Glenn L. Millhauser
Department of Chemistry & Biochemistry
UC Santa Cruz
Santa Cruz, CA 95064
831 459 2176 voice
831 566 3337 cell
831 459 2935 fax

http://chemistry.ucsc.edu/~glennm
http://www.chemistry.ucsc.edu/faculty/millhauser.html


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