Reading density files in xyz format
I’ve run an Amber trajectory and generated grid data as a volumetric map. The density is calculated by treating each atom as a 3-dimensional Gaussian function whose standard deviation is equal to the van der Waals radius. The format of the file is xyz (see head of the file below). 727 C 3.46464014 25.54114723 39.11305046 0.03241467 C 3.46464014 26.54114723 40.11305046 0.03353754 C 3.46464014 28.54114723 40.11305046 0.03223133 C 3.46464014 29.04114723 37.61305046 0.03259914 C 3.46464014 30.04114723 41.11305046 0.03254872 C 3.46464014 31.54114723 28.11305046 0.03995054 C 3.46464014 32.04114723 38.11305046 0.02878203 C 3.46464014 33.04114723 42.61305046 0.02801451 Is there a way to visualise in Chimera the protein together with volumetric map? Thank you in advance for any advice George
Hi George, Did you know that the MD Movie (trajectory viewer) tool has an option to calculate this kind of map from the trajectory? Then it is automatically visualized using Volume Viewer in Chimera. See “occupancy analysis” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...> Maybe the trajectory was too big for Chimera, or there was some other reason you didn’t do it that way. Nevertheless, you would need to write the data in a format that Chimera can understand. Chimera reads a lot of different density-map formats: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html> ... but what you showed is not one of them, as far as I can tell. There is an XYZ format but it is for atoms: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/xyz.html> Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 14, 2017, at 10:36 AM, George Tzotzos <gtzotzos@me.com> wrote:
I’ve run an Amber trajectory and generated grid data as a volumetric map. The density is calculated by treating each atom as a 3-dimensional Gaussian function whose standard deviation is equal to the van der Waals radius. The format of the file is xyz (see head of the file below).
727
C 3.46464014 25.54114723 39.11305046 0.03241467 C 3.46464014 26.54114723 40.11305046 0.03353754 C 3.46464014 28.54114723 40.11305046 0.03223133 C 3.46464014 29.04114723 37.61305046 0.03259914 C 3.46464014 30.04114723 41.11305046 0.03254872 C 3.46464014 31.54114723 28.11305046 0.03995054 C 3.46464014 32.04114723 38.11305046 0.02878203 C 3.46464014 33.04114723 42.61305046 0.02801451
Is there a way to visualise in Chimera the protein together with volumetric map?
Thank you in advance for any advice
George
There is a Python script on the Chimera scripts page called xyzsdmap.py that does this with a slightly different file (no first column C, and 3 columns for sdev). http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> You could edit the file, and use that script. Tom
On Sep 14, 2017, at 10:36 AM, George Tzotzos wrote:
I’ve run an Amber trajectory and generated grid data as a volumetric map. The density is calculated by treating each atom as a 3-dimensional Gaussian function whose standard deviation is equal to the van der Waals radius. The format of the file is xyz (see head of the file below).
727
C 3.46464014 25.54114723 39.11305046 0.03241467 C 3.46464014 26.54114723 40.11305046 0.03353754 C 3.46464014 28.54114723 40.11305046 0.03223133 C 3.46464014 29.04114723 37.61305046 0.03259914 C 3.46464014 30.04114723 41.11305046 0.03254872 C 3.46464014 31.54114723 28.11305046 0.03995054 C 3.46464014 32.04114723 38.11305046 0.02878203 C 3.46464014 33.04114723 42.61305046 0.02801451
Is there a way to visualise in Chimera the protein together with volumetric map?
Thank you in advance for any advice
George
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Tom, Elaine Many thanks. Appreciated as always. George
On 14 Sep 2017, at 21:04, Tom Goddard <goddard@sonic.net> wrote:
There is a Python script on the Chimera scripts page called xyzsdmap.py that does this with a slightly different file (no first column C, and 3 columns for sdev).
http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>
You could edit the file, and use that script.
Tom
On Sep 14, 2017, at 10:36 AM, George Tzotzos wrote:
I’ve run an Amber trajectory and generated grid data as a volumetric map. The density is calculated by treating each atom as a 3-dimensional Gaussian function whose standard deviation is equal to the van der Waals radius. The format of the file is xyz (see head of the file below).
727
C 3.46464014 25.54114723 39.11305046 0.03241467 C 3.46464014 26.54114723 40.11305046 0.03353754 C 3.46464014 28.54114723 40.11305046 0.03223133 C 3.46464014 29.04114723 37.61305046 0.03259914 C 3.46464014 30.04114723 41.11305046 0.03254872 C 3.46464014 31.54114723 28.11305046 0.03995054 C 3.46464014 32.04114723 38.11305046 0.02878203 C 3.46464014 33.04114723 42.61305046 0.02801451
Is there a way to visualise in Chimera the protein together with volumetric map?
Thank you in advance for any advice
George
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participants (3)
-
Elaine Meng -
George Tzotzos -
Tom Goddard