[Chimera-users] seelction around map

Dhiraj Srivastava dhirajks at gmail.com
Fri Sep 7 16:07:07 PDT 2007

Hi Tom
          actually i calculated the cavity inside my protein through voidoo
and it gives me a map. so i was trying to see residues lining the cavity. i
was not aware that voidoo gives us list of atoms lining the cavity in its
log file. any way i looked in the log file and found the residue. i manually
selected the residue (about 100) and make the figures. but it is nice if i
can do it by computers without typing the resid of about 100 residue.

Thank you.

On 9/7/07, Tom Goddard <goddard at cgl.ucsf.edu> wrote:
> 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:
>    http://www.cgl.ucsf.edu/chimera/experimental/experimental.html
> Tom

Dhiraj K. Srivastava
Department of Chemistry
University of Missouri-Columbia
MO, 65211
Ph. no. 001-573-639-0153
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