Hi Jeff, There are two general reasons why the *displayed* marker radius and link radius might not equal the values shown in Volume Path Tracer. In the following explanation, atom = marker and bond = link. (1) The atom or marker is in the "ball" representation rather than "sphere." displayed ball radius = (ball scale)(atom radius) where the default ball scale is 0.25. You could - change the atom to the "sphere" representation, which uses the full radius. "Actions... Atoms/Bonds... sphere" or the command "repr sphere sel" will change the selected atoms to the sphere representation. or - stay in the "ball" representation but change the "ball scale" factor to 1.0 (I'll describe how to get to this parameter below) (2) Similar to the markers, displayed bond or link radius = (stick scale)(bond radius) You could make sure that the "stick scale" factor is 1.0. It probably already is, since that's the default. Of course, the bond or link should also be the stick representation, not wire. Volume Path Tracer automatically makes them sticks when the radius is >0, however. In the Model Panel, if you click the IMOD contours model (or any molecule model) on the left and "attributes..." on the right (or just double-click the model on the left), that opens the molecule model attributes panel. In there you can see and change the ball scale and stick scale values. In your example file trial2.mod, I selected a few markers and links and set all their radii to 20. After I changed the marker to sphere, it did match up in size with the connected link. The more I zoomed in, the better it looked. It may be a level of detail issue if they don't look matched up when zoomed out. You can increase the number of subdivisions used to draw the spheres/cylinders with subdivision quality in Effects (under Tools... Viewing Controls). The parallel links did not quite touch, however, but since you said the contours were approximately 40 A apart, I think it is working correctly! If you still have trouble, though, let me know. 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 Jun 7, 2007, at 12:12 PM, William Jeffrey Triffo wrote:
thanks Elaine,
another thing I noticed, when I change the marker (atom?) radius in Volume Path Tracer, it does not appear to change quite right. For instance, if I set the 'Link' radius to something like '20', and likewise the Marker radius to '20', they will not be the same size.
In general when making marker sets, this is not the case, and the radius acts the same between the two settings. For these markers, the contours were place approx. 40 A apart, so a marker (or link) radius of '20' should make the contours 'kiss' when viewed as a marker set, correct?
thanks for your prompt response, it would make sense that I would miss the color setting instructions on the actual page for the tool...
-Jeff