[Chimera-users] Reading density files in xyz format

Tom Goddard goddard at sonic.net
Thu Sep 14 11:04:44 PDT 2017


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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