[Chimera-users] Reading density files in xyz format

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 14 10:54:39 PDT 2017


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.html>

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 at 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




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