[Chimera-users] Chimera Settings

[Elaine Meng]

Hi Nuwan,
You cannot set a preset as a default. A preset is something that you run after open the structure(s).

About the silhouettes and depth-cueing settings in Effects (Tools… Viewing Controls… Effects), you have to make the settings like you want and then remember to click Save so that they will be the default in later uses of Chimera. These settings are also remembered in a session file, so if you open a session file it will change to the settings that were present when you saved the session file.

I do not know python myself, but you can open python files just like other Chimera input files on any platform.  Here are instructions on how to write python for looping through structure files and applying Chimera commands to them.  
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

Of course, that would require you to first figure out the Chimera commands you want to run on each structure.  Chimera commands:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

See also “image tips”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/print.html#tips>
...and  Chimera tutorials:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>

 I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 25, 2018, at 11:17 AM, Nathan Randall <nathan2017store at gmail.com> wrote:
> 
> Hi Elaine,
> 
> Do you have a python script that loops through bunch of files and display chimera output that I can run from a terminal? If so, do I need to install the linux version of chimera?
> 
> And also, I was not able to set the following preset as default: 
> Presets —> Select Publication 1
> 
> According your previous email reply I was able to set the background color to white. But I could not reproduce the silhouettes and depth-cueing effect.
> 
> Thank you,
> Nuwan
> 
>> On May 18, 2018, at 3:49 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Nuwan,
>> If you are really done viewing the molecule, you should close it  (e.g. command: close #0) or close the session (e.g. menu: File… Close Session).  You do not need to quit from Chimera, if that’s what you meant.
>> 
>> You could just hide the molecule instead of closing it, but that would be the same amount of work.  The only reason to hide it is if you want to work with multiple structures together but temporarily hide one or the other.  You can hide/show open models with Model Panel (open from Favorites menu, use “S” checkbox).  You can also use the Model Panel to close a specific model.
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
>> 
>> You may want to try the “getting started” tutorial to become more familiar with Chimera; it explains stuff like this.
>> <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On May 18, 2018, at 9:57 AM, Nuwan DeSilva <nathan2017store at gmail.com> wrote:
>>> 
>>> Hi Elaine,
>>> 
>>> I have another question.
>>> 
>>> When I open a file and after done viewing the file (lets say molecule 1), I want to open another file (lets say molecule 2). Each time I have to close the sessions and open the molecule 2. Otherwise molecule 2 will display on top of the molecule 1. How can I set  that display only the new molecule (molecule 2)?
>>> 
>>> Thank you,
>>> Nuwan
>> 
>> 
>> 
>> 
>> 
>> 
> 
> 
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