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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