[Chimera-users] seelction around map

Tom Goddard goddard at cgl.ucsf.edu
Fri Sep 7 15:30:58 PDT 2007

Hi Dhiraj,

  A couple questions?  What do you mean by "around 3.2A of channel or 
map"?  Do you mean distance from the atom to the nearest contour surface 
point?  That would would include all the atoms near the map, even those 
far from the portal.  Do you also want to restrict to 3.2A of the 
portal?  How do you define that?  Does it mean 3.2A from the z axis 
(treating the portal like a straight line)?  Or have you already limited 
the selection to ions in the channel and you just want to know which of 
them is within 3.2A of the contour surface?

  Please describe your problem in more detail.

  There is a tool on the Chimera experimental features page that you can 
download separately that measures distances from atoms to surfaces.  
That may be of use although it is not able to select the atoms within a 
given distance.  The code could be easily modified to achieve that.  It 
is called "Distance to Surface" and is available on this page:



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