From: Xinqiang Ding (
Date: Tue Dec 16 2014 - 20:32:58 CST


Thanks for your explanation.

Actually what I want to do is to cut out part of electron density map. But in order to do that using volatil command (also from vmd), I have to give it the six coordinates (minx, miny, minz, maxx, maxy, maxz), which defines the box region I want. So I want to get these coordinates.

Is there a better way to do it?


> On Dec 16, 2014, at 9:23 PM, John Stone <> wrote:
> Hi,
> The way that 3-D picking works is to imaging that when you select a
> point on the 2-D screen, a ray with an origin at the camera position is
> generated, and this ray is tested for intersection against geometry
> shown on the display. The nearest geometry shown on the display that
> is intersected by this picking-test ray is then considered to be "picked",
> and VMD (or any similar program) proceeds by figuring out what "object"
> (an atom in the case of VMD) was associated with the geometry that was
> "picked". In the case that you don't have an atom or associated graphics
> geometry shown, then you would have nothing for the picking test to
> intersect the ray with, so there isn't a 3-D cartesian coordinate
> associated with the picking operation. If you want to compute the ray
> that would be associated with a mouse picking operation over an area
> of empty space, that can be done with some linear/matrix algebra using
> the VMD viewing matrices. If you only want the 2-D screen space coordinate
> associated with the mouse pick, that is available through a simple scripting
> callback when the mouse is set to "user" mode. Let me know if any of these
> is what you're looking for.
> Cheers,
> John Stone
> On Tue, Dec 16, 2014 at 06:11:48PM -0500, Xinqiang Ding wrote:
>> Dear all,
>> How can we get the coordinate of the mouse arrow in VMD? I know that if there is an atom, we can select that atom, then see their coordinates using label. But how can I get the coordinate of the point which the mouse arrow is pointing to and there is no atom there?
>> Thank a lot,
>> Xinqiang
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Phone: 217-244-3349

Xinqiang Ding
PhD student at Brooks Lab
Department of Computational Medicine and Bioinformatics
University of Michigan