[Chimera-users] Reading density files in xyz format

[George Tzotzos]

Tom, Elaine 

Many thanks. Appreciated as always.

George

> On 14 Sep 2017, at 21:04, Tom Goddard <goddard at 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
>> 
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170914/478fdb69/attachment.html>