Hi, 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, Nuwan
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. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules> 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 findhbond 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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets> 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 16, 2018, at 1:08 PM, Nuwan De Silva <nuwan.desilva@wne.edu> wrote:
Hi, 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, Nuwan
Hi Elaine, Thank you very much. This is very helpful. Nuwan
On May 16, 2018, at 6:53 PM, Elaine Meng <meng@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. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules>
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 findhbond 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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets>
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 16, 2018, at 1:08 PM, Nuwan De Silva <nuwan.desilva@wne.edu> wrote:
Hi, 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, Nuwan
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
On May 16, 2018, at 6:53 PM, Elaine Meng <meng@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. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules>
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 findhbond 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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets>
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 16, 2018, at 1:08 PM, Nuwan De Silva <nuwan.desilva@wne.edu> wrote:
Hi, 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, Nuwan
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@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
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@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@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
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@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@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@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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Hi Elaine, Do you know how to show vibrational mode vectors (arrows) for each vibrational mode from chimera? Nuwan ________________________________ From: Nuwan De Silva Sent: Friday, May 18, 2018 12:57:49 PM To: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Chimera Settings 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
On May 16, 2018, at 6:53 PM, Elaine Meng <meng@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. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%20Molecules>
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 findhbond 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: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Presets>
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 16, 2018, at 1:08 PM, Nuwan De Silva <nuwan.desilva@wne.edu> wrote:
Hi, 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, Nuwan
Hi Nuwan, I changed the subject line to something more descriptive. If you mean does Chimera calculate these vectors, no it does not, sorry. If you mean displaying vectors in 3D that were calculated in some other program, please see this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012116.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 Apr 24, 2019, at 12:33 PM, Nuwan De Silva <nuwan.desilva@wne.edu> wrote:
Hi Elaine,
Do you know how to show vibrational mode vectors (arrows) for each vibrational mode from chimera?
Nuwan
Hi Elaine, I just want to display the vectors that are calculated from gamess quantum chemistry program. Nuwan
On Apr 24, 2019, at 6:24 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
**** EXTERNAL MESSAGE ****
Hi Nuwan, I changed the subject line to something more descriptive.
If you mean does Chimera calculate these vectors, no it does not, sorry.
If you mean displaying vectors in 3D that were calculated in some other program, please see this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012116.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 Apr 24, 2019, at 12:33 PM, Nuwan De Silva <nuwan.desilva@wne.edu> wrote:
Hi Elaine,
Do you know how to show vibrational mode vectors (arrows) for each vibrational mode from chimera?
Nuwan
participants (4)
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Elaine Meng -
Nathan Randall -
Nuwan De Silva -
Nuwan DeSilva