[Chimera-users] IMOD mesh/surface colors

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 7 13:15:34 PDT 2007

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  
     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.
- 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,  

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 C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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

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