Hi, Sorry there was a typo in the last message! The centroid feature is great, but I would like to select two centroids or a centroid and an atom and then measure the distance between them. When I try this I get the Error Message: "Exactly two atoms must be selected in the graphics window". Is there anyway to add the ability to make these measurements. Thanks, Dave -------------------------------------------------------- David Chenoweth NIH Postdoctoral Fellow Swager Research Group Massachusetts Institute of Technology Chemistry Department, 18-053 77 Massachusetts Avenue Cambridge, MA 02139 Email: dcheno@mit.edu Lab Phone: 617-258-6537 --------------------------------------------------------
Hi David, Definitely, the centroids are designed to be used in distance measurements to each other and to atoms, axes, and planes. Distance measurements between any pair of objects (centroids, axes, planes) can be made using either the Axes/Planes/Centroids tool or the distance command. The Distances tool, however, is only for distance monitors between atoms, not objects. to use Axes/Planes/Centroids tool: choose any two objects in the list (click the line for one and ctrl- click the line for the other, or you can just drag if they are adjacent), which will automatically give the distance in that dialog and in the Reply Log. To measure atom-object distances, select the atoms and then in the Axes/Planes/Centroids dialog, choose the object and click the "Report distance" button. to use the "distance" command: include the IDs of the objects, which are shown in the Axes/Planes Centroids tool, in the command. For example: dist c1 c2 We plan to allow using the command "dist sel" if two centroids, or one atom and one centroid, etc. are selected in the graphics window, but that has not been implemented yet. I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 20, 2010, at 7:42 AM, David Chenoweth wrote:
Hi, Sorry there was a typo in the last message! The centroid feature is great, but I would like to select two centroids or a centroid and an atom and then measure the distance between them. When I try this I get the Error Message: "Exactly two atoms must be selected in the graphics window". Is there anyway to add the ability to make these measurements.
Thanks, Dave
On Feb 20, 2010, at 10:09 AM, Elaine Meng wrote:
to use the "distance" command: include the IDs of the objects, which are shown in the Axes/Planes Centroids tool, in the command. For example: dist c1 c2
We plan to allow using the command "dist sel" if two centroids, or one atom and one centroid, etc. are selected in the graphics window, but that has not been implemented yet.
I forgot to mention that it does already work to use "sel" for just the atom, so you could also use: dist c1 sel to measure the distance between centroid c1 and a single selected atom, or instead of selecting anything, you could just give the specification of that atom, for example: dist :14.a@ca c1 Elaine
Hi Elaine, I figured there had to be a way to do this! Thanks for your help, Dave On Feb 20, 2010, at 1:15 PM, Elaine Meng wrote:
On Feb 20, 2010, at 10:09 AM, Elaine Meng wrote:
to use the "distance" command: include the IDs of the objects, which are shown in the Axes/Planes Centroids tool, in the command. For example: dist c1 c2
We plan to allow using the command "dist sel" if two centroids, or one atom and one centroid, etc. are selected in the graphics window, but that has not been implemented yet.
I forgot to mention that it does already work to use "sel" for just the atom, so you could also use:
dist c1 sel
to measure the distance between centroid c1 and a single selected atom, or instead of selecting anything, you could just give the specification of that atom, for example:
dist :14.a@ca c1
Elaine
participants (2)
-
David Chenoweth -
Elaine Meng