[Chimera-users] Chimera Settings
Nuwan De Silva
nuwan.desilva at wne.edu
Wed Apr 24 12:33:00 PDT 2019
Do you know how to show vibrational mode vectors (arrows) for each vibrational mode from chimera?
From: Nuwan De Silva
Sent: Friday, May 18, 2018 12:57:49 PM
To: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] Chimera Settings
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)?
> On May 16, 2018, at 6:53 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Nuwan,
> Certain global settings should stay the same if you don’t quit from Chimera: background color and whether or not outlines (“silhouettes”) and depth-cueing are used should stay the same unless you change them or quit from Chimera.
> For quitting/restarting, you can keep background color same by using the Preferences (open from Favorites menu), category: Background. Set the color by clicking the square in that dialog and then click Save if you want it to apply to later uses of Chimera. You can keep silhouettes and depth-cueing the same by clicking Save on the Effects tool (open with menu: Tools… Viewing Controls… Effects).
> You can keep molecular style the same also using the Preferences, category: New Molecules. You would have to turn off “smart initial display” (but then ALL atoms will be shown instead of just the binding sites) and then change “atom style” to “ball” and “bond style” to “stick.” Take a look at the other choices in that dialog and see if you also want to change anything else (for example, you probably want to set “per-atom coloring” to “by heteroatom”). Again, remember to click Save if you want the settings to be remembered when you quit and restart Chimera.
> However, there is no way to automatically calculate H-bonds every time you open an atomic structure.
> If you don’t want to display all atoms, but just the binding sites like the smart initial display, you could make your own preset that does all 3 of your steps, for example with a command file containing:
> preset apply pub 1
> repr bs
> … (findhbond could also have any command options that you want, like the color of the lines) but you would have to run the preset after opening a structure (it wouldn’t run automatically). After creating that file you can specify it as a preset to include in the Presets menu by using the Preferences again (category: Presets), see:
> I hope this helps,
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On May 16, 2018, at 1:08 PM, Nuwan De Silva <nuwan.desilva at wne.edu> wrote:
>> Every time when when I open a file my background color, and presets, changes. I want to keep them same for every time. How can I set these things?
>> For example, I wanted to have
>> A) Presets —> Select Publication 1
>> B) Tools —> Structure —> Find H bonds
>> C) Actions —> Atoms & Bonds —> Balls & Sticks
>> Thank you,
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