[Chimera-users] molecular surface el. potential data

[Tom Goddard]

Hi Marek,

  Ok, open the attached Python script file in Chimera and it will add a command surfvalues that will write map values at surface points to a text value.  For example,

	surfvalues #0 #1 ~/Desktop/values.txt

where #0 is a surface and #1 is volume data writes a file

#        x          y          z       area      value
    1.3803     1.3727     3.5524    0.65338   0.094239
     1.852    0.58549     4.5782    0.67751   0.038903
    1.7432     1.5464     4.0689    0.61585   0.018199
    3.3341   -0.65998     3.3031    0.40357  -0.051493
    3.0674  -0.044984      2.101    0.54381  -0.018439


The first 3 columns are the coodinates of the surface point, the 4th column is the surface area associated with that point, and the last column is the map value at that point using trilinear interpolation.

	Tom

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> On Jul 3, 2016, at 3:22 PM, Marek Maly <marek.maly at ujep.cz> wrote:
> 
> Hello,
> 
> Chimera has capability to color molecular surface by electrostatic potential (including solvent, ions effect) using data calculated on relevant volume grid (eventually saved in *.dx file) by apbs module.
> My question is, is/could be possible simply to export el. potential values which are on the molecular surface (that which are using for surface coloring) to *.txt file for consequent processing - e.g. calculation of the average value of the el. potential on the molecular surface, standard deviation ... ?
> 
>   Best wishes,
> 
>        Marek
> 
> -- 
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