[Chimera-users] vector from atom

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 29 10:52:39 PDT 2016

Hi Fabian,
Not sure I understand the exact problem, but I’m guessing the MD program takes as input some vector to apply force, and you are trying to figure out what to use as that vector.

Chimera won’t figure out where the exit tunnel is, so first you would need to know yourself which direction that is. Then, maybe you could open a structure that is just two fake atoms several angstroms apart connected by one fake bond (I attach a PDB file of such a model).  Then, you can move that long “stick” separately from the original structure to manually position it in the direction of the exit tunnel (with the  “Active models” checkboxes below the Command Lne or the “A” checkboxes in the Model Panel, you can activate/deactivate models for movement with the mouse, so that they can be moved separately. Command Line or Model Panel can be shown using the Favorites menu).

If the stick is too short or long, you can select it and change its length in the Adjust Bonds panel of Build Structure (in menu under Tools… Structure Editing).

Then save the simple stick model to a PDB file (menu: File… Save PDB), making sure to save it “relative to” the other structure.  In the resulting PDB file, the coordinates of the two fake atoms will define the vector, i.e. subtract x,y,z of one fake atom from the other to get vector x,y,z.  Which you subtract from which depends on the direction of the vector.  You can label the simple stick model in Chimera to see which atom is on which end.

This might be a crazy idea or too much work, though.
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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On Jun 29, 2016, at 7:26 AM, Fabian gmail <fabian.glaser at gmail.com> wrote:

> Hi,
> I have an ion in a membrane transporter which I am simulating in MD, now, I need in order to pull the ion outside the transporter to use a vector to identify a water molecule which is exactly in the direction of the exit tunnel. For that purpose I need to draw such a vector or to at least identify a water molecule in the right direction. Can Chimera help me with that?
> I mean is there a way to identify which water is on the exact pathway of the ion exit?
> How can I do it?
> Thanks a lot in advance,
> Fabian

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