[Chimera-users] vector from atom
meng at cgl.ucsf.edu
Wed Jun 29 15:14:07 PDT 2016
You can draw a line between any two atoms (by distance measurement, for example), or if you already know the endpoint coordinates, you can create a 3D arrow in BILD format and then read it in. However, if I understand correctly, the problem is that you do not already know what the other atom is or the direction of the vector. In that case you would have to use one or more fake atoms (like the stick.pdb sent in the previous message, or one fake atom with distance measurement between it and your ion) and manually position it to the direction you want. Then you could see if it crosses any waters that are already in your system.
On Jun 29, 2016, at 11:44 AM, fglaser at techunix.technion.ac.il wrote:
> Hi Elaine,
> Thanks a lot for your detailed answer, I think I did not explain myself good enough, I just want to find a water molecule far away from tunnel exit, which I can easily identify, and use that water to pull the ion from the tunnel towards it. I would prefer to avoid dummy atoms into the simulation if possible.
> So the only thing I want from chimera is to visualize a vector from the ion inside the tunnel (the ion is present in the Pdb) towards the exit (which I can easily identify) and in that way to identify a water molecule in the path of that vector to use as a kind of dummy atom (it will not move during simulation). That is it.
> So is there a way to draw or visualize a vector from an atom in chimera to a certain direction? In this way I will be able to find my water molecule far from the tunnel entrance.
> Thanks a lot,
> Sent from myMail app for Android
> Wednesday, 29 June 2016, 08:52PM +03:00 from Elaine Meng meng at cgl.ucsf.edu:
> 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
> 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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