adding measurement to Angles/Torsions via command line
Hi,
Is there a way to add a torsion measurement to the Angles/Torsions table via command line so that i can create a .com file to more easily analyze multiple measurements upon opening my session?
The best workaround I can think of is to just use the 'angle' command followed by 'start Reply Log'.
Thanks,
ryan
Hi Ryan, Since the Angles/Torsions table does little but list the values, we didn’t see added value in putting “angle” results there instead of (or inaddition to) putting them in the Reply Log. The Reply Log also has a Save button to save its contents to a text file.
I guess the Angles/Torsions dialog does allow you to select the atoms/bonds for each angle by clicking in the table. Are you reyling on that feature? If not, might as well use the Reply Log. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 28, 2018, at 2:12 PM, Ryan Pavlovicz pavlo2@gmail.com wrote:
Hi, Is there a way to add a torsion measurement to the Angles/Torsions table via command line so that i can create a .com file to more easily analyze multiple measurements upon opening my session? The best workaround I can think of is to just use the 'angle' command followed by 'start Reply Log'. Thanks, ryan
Hi Elaine,
Thanks for the quick reply! The Reply Log method will work for what I need, but being able to highlight the measured angles would help the visual analysis when considering a bunch of different measurements in a single session. For now, I'm just looking at few angles, so it's not too hard to remember the order in which they are measured/reported to the Reply Log.
Thanks again,
ryan
On Thu, Jun 28, 2018 at 3:48 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Ryan, Since the Angles/Torsions table does little but list the values, we didn’t see added value in putting “angle” results there instead of (or inaddition to) putting them in the Reply Log. The Reply Log also has a Save button to save its contents to a text file.
I guess the Angles/Torsions dialog does allow you to select the atoms/bonds for each angle by clicking in the table. Are you reyling on that feature? If not, might as well use the Reply Log. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 28, 2018, at 2:12 PM, Ryan Pavlovicz pavlo2@gmail.com wrote:
Hi, Is there a way to add a torsion measurement to the Angles/Torsions table
via command line so that i can create a .com file to more easily analyze multiple measurements upon opening my session?
The best workaround I can think of is to just use the 'angle' command
followed by 'start Reply Log'.
Thanks, ryan
After some reflection, we do see some value to the table in that it’s nicer looking, easier to read, and doesn’t scroll away from what you’re interested in. However, there is no Chimera command for adding an entry to that table. The Python for doing so isn’t too complicated though. I’ve attached a Python file that adds two torsion measurements for any single-chain structure (e.g. 1gcn). I think it’s pretty obvious where the atom specs are and how you add additional measurements. You run it simply by opening it with File→Open or the “open” command.
—Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 28, 2018, at 3:48 PM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Ryan, Since the Angles/Torsions table does little but list the values, we didn’t see added value in putting “angle” results there instead of (or inaddition to) putting them in the Reply Log. The Reply Log also has a Save button to save its contents to a text file.
I guess the Angles/Torsions dialog does allow you to select the atoms/bonds for each angle by clicking in the table. Are you reyling on that feature? If not, might as well use the Reply Log. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 28, 2018, at 2:12 PM, Ryan Pavlovicz pavlo2@gmail.com wrote:
Hi, Is there a way to add a torsion measurement to the Angles/Torsions table via command line so that i can create a .com file to more easily analyze multiple measurements upon opening my session? The best workaround I can think of is to just use the 'angle' command followed by 'start Reply Log'. Thanks, ryan
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participants (3)
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Elaine Meng -
Eric Pettersen -
Ryan Pavlovicz