Hi Gabor, I am pretty sure the capabilities are still there, but maybe the dialog has been rearranged - In the Volume Viewer dialog, choose Features... Atom box - is that what you had in mind? <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volume...
Another possibility is to use Features... Zone to get everything within some distance of your markers (not necessarily a rectangular box): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volume...
For both of those, you would first need to select all the markers of interest. To get the (untransformed) coordinates of the markers, you could save them to a file from the Volume Tracer tool, or select them and use the command: getcrd sel which sends the coordinates to the Reply Log (under Favorites). Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 26, 2009, at 4:43 AM, Gabor Papai wrote:
Hi,
I would like to do the following: I placed markers on density spots. I want to get their coordinates and excise a box around the marked density and save it as a separate file. For this I would like to know how I can retrieve the coordinates of a marker set and possibly how to position exactly a box around a marker to set a subregion (and of course how to set the dimensions of that box). This second feature existed before, but disappeared in the latest releases with the subregion selection tool in the Volume Viewer. Thanks in advance, Gabor