[Chimera-users] MD plots

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 5 13:18:09 PST 2011

Hi George,
The distance command is for showing the distance monitor (dashed line and angstrom label).  For MD movie plotting,  you need only select the two atoms and then click the Plot button on the dialog.  In the image you sent, the dialog is showing an error message that suggests you do not have exactly two atoms selected (i.e. either fewer or more atoms than two seem to be selected).   Try clearing the selection before you select the two atoms.  Also make sure your selection is really getting only two atoms. 

For example, realize ":124 at H" could select more than one atom.  There might be residue 124 in both chain A and chain B, and/or in model 0 and model 1, etc.

You can see how many atoms are selected, for example by clicking the green magnifying glass on the lower right corner of the Chimera window to open the Selection Inspector.
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

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