VMD-L Mailing List

From: Mark Cunningham (cunningham_at_utpa.edu)
Date: Sun Mar 14 2010 - 14:45:21 CDT

We are conducting some IMD simulations with a Phantom Omni and

I have noticed that the position output of the Omni seems to be mapped

to the internal XYZ coordinates of VMD. I have positioned the protein

and its substrates into a configuration in which things are more readily

visible, which results in a display in which the internal XYZ is
rotated.

It is difficult to manipulate the Omni because physical up<->down may

correspond to in<->out or left<->right (or some combination thereof) in

the virtual device on the screen.

 

Is there a mechanism to allow the virtual device to follow the external

XYZ coordinates and not interpret them as internal XYZ? This would,

I believe, simplify the interface for the operator: up<->down motion of
the

haptic device results in up<->down motion of the virtual device.

 

Secondly, is there a means for forcing an intramolecular dihedral
rotation

with IMD? I can do so with tclForces but have observed that the rotate

tool forces the entire molecule or selection to rotate.

 

Thanks for your help,

 

Mark