Adding quadrant lines to atoms
Hi, Is there a way to add quadrant lines to atoms similar to how Houkview does it in CylView, pictured below. If not, could you add this feature as an option? All the best, Trevor Harris
Hi Trevor, There isn’t a direct way to do it, but Chimera’s Thermal Ellipsoids tool (in the Structure Analysis category) has this depiction for structures with anisotropic B-factor information (ANISOU records in PDB files). If your structure doesn’t have such information, you can add fake information to the structure and fool Thermal Ellipsoids into rendering the depiction. The following Python code will add fake anisotropic B-factor information to the structures atoms: import numpy import chimera for a in chimera.openModels.list()[0].atoms: a.anisoU = numpy.identity(3, dtype=numpy.float32) * a.radius I have attached a file with the above Python in it. Just open the file after you open your structure. Then with the Thermal Ellipsoids tool you should be able to get something like this: You would use the “Octant lines” preset of the tool. I also changed the scale factor in the tool to 0.25. To get the black bonds, select the whole structure (Select->Select All) and then bring up the Selection Inspector (magnifying-glass icon at the bottom right of the Chimera window). Change the Inspect category to “Bond”, and then “halfbond mode” to “off”, “radius” to 0.1, and “color” to black. You can change the background to white either with the command “set bgcolor white” or Actions->Color->all actions… and in the resulting dialog change “…applies to” to “background” and click on white. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 19, 2018, at 2:26 PM, Trevor Harris <trevorha@sas.upenn.edu> wrote:
Hi,
Is there a way to add quadrant lines to atoms similar to how Houkview does it in CylView, pictured below. If not, could you add this feature as an option? <PastedGraphic-3.tiff> All the best, Trevor Harris _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks, unfortunately I already have my own preset information saved as a a command file and when I go to open my preset it won’t recognize this new information obviously. Is there a way to get this information as command information instead? Trevor
On Apr 19, 2018, at 7:38 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
<aniso.py>
Hi Trevor, There is an “aniso” command to show thermal ellipsoids. It doesn’t know the thermal-ellipsoid presets per se, but there are keyword options for all of the settings, so you could get to the same result as a given preset by combining those options. Details on “aniso” and its options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/aniso.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 19, 2018, at 9:08 PM, Trevor Harris <trevorha@sas.upenn.edu> wrote:
Thanks, unfortunately I already have my own preset information saved as a a command file and when I go to open my preset it won’t recognize this new information obviously. Is there a way to get this information as command information instead?
Trevor
On Apr 19, 2018, at 7:38 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
<aniso.py>
P.S. …and you can use the “open” command to open the python file Eric sent Elaine
On Apr 20, 2018, at 10:12 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Trevor, There is an “aniso” command to show thermal ellipsoids. It doesn’t know the thermal-ellipsoid presets per se, but there are keyword options for all of the settings, so you could get to the same result as a given preset by combining those options.
Details on “aniso” and its options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/aniso.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 19, 2018, at 9:08 PM, Trevor Harris <trevorha@sas.upenn.edu> wrote:
Thanks, unfortunately I already have my own preset information saved as a a command file and when I go to open my preset it won’t recognize this new information obviously. Is there a way to get this information as command information instead?
Trevor
On Apr 19, 2018, at 7:38 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
<aniso.py>
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participants (3)
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Elaine Meng -
Eric Pettersen -
Trevor Harris