Hi Dhiraj, You can select just the atoms in a map with some Chimera black magic. There is a keyboard shortcut "oa" that restricts the currently selected set of atoms to those that are above the threshold level of the volume data set shown in the volume dialog. If you start by selecting all atoms (menu Select / Select All or shortcut "sa") then use "oa" then you have the atoms outside the map selected, then invert the selection (menu Select / Invert or shortcut "is"). These Chimera shortcuts need to be enabled using menu entry Tools / General Controls / Accelerators On, and then you can type the two letter key sequences into the main Chimera window. Here's a list of other shortcuts. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.... Tom

Hi Dhiraj, Here is an idea: You could use "Values at Atom Positions" to interpolate map values onto the atoms and then select sets of atoms based on those values. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/density/ density.html For example if you had open the data mymap.ccp4 and a structure, you could use Values at Atom Positions to assign an attribute to all the atoms, named by default value_mymap_ccp4. Atoms outside the bounds of your data will be assigned attribute values of zero. You could select all the atoms with attribute values less than, greater than, or equal to some value, for example: Command: select @/value_mymap_ccp4>5.0 I have no idea what value would work in your case, but maybe with some experimentation you could get all atoms reasonably near to some density that are also inside the bounds of the density map. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Sep 7, 2007, at 1:07 PM, Dhiraj Srivastava wrote:

Hi all        Is there any way that we can select atoms or residues within some distance of a ccp4 map in chimera? i know tha we can select map within some distance of any selected atoms but can we do opposite and if yes then how?

thank you Dhiraj -- Dhiraj K. Srivastava Department of Chemistry University of Missouri-Columbia MO, 65211 Ph. no. 001-573-639-0153_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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