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. Dhiraj On 9/7/07, Tom Goddard <goddard@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