[Chimera-users] Select model based on its position and orientation

[Yu Zhou]

 Elaine,
Thank you so much for your help.
The "sel up" does the trick.
Yu 
    On Wednesday, September 29, 2021, 01:02:11 PM CDT, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 
 Dear Yu Zhou,
I wouldn't call it "automatic"  ... you would have to figure out (by trial and error) some measurements that would distinguish the interesting ones from the others.  It would probably be some combination of distance zones, or distance zone plus angle measurement.  

E.g. some specific atoms of protein A must be within distance X of some specific atoms of protein B, and the crossing angle of an axis defined from some atoms of A with the axis defined from some atoms of B must be smaller than Y.  See command-line distance zone specification and commands "define" (define axis) and "angle" (measure angle between axes).

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

Once you figure out commands that distinguish the classes of solutions, then you would need to script going through the docking solutions and keeping or discarding them.  If for all the dockings one protein stays in the same place and only the other one moves, you might be able to do it interactively by entering the commands in the Chimera command line.  Otherwise, you would need to script with Python to loop through the different A-B positions, see:
<https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

For example, in the case where one protein (say #0) is always in the same place but #1.1, #1.2, #1.3 (etc.) are the dockings of the other protein, then this would select the dockings that have residue 123 more than 8 angstroms from residue 10 in #0. 

select #1:123 & #0:10 za<8

If that was reason enough for you to discard the solutions, you could increase selection to whole models (e.g. all atoms of #1.3) and delete those docked positions, e.g.

sel up
delete sel

You might need to use "sel up" more than once depending on what's in your docked models #1.1, #1.2, ...  For angle measurements you wouldn't select in the same command, you'd have to use the "angle" command to measure and then decide (interactively or in the script) whether to discard the solution based on the result.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 29, 2021, at 8:59 AM, Yu Zhou via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear all,
> 
> I tried global docking of two proteins and ended up with hundreds of possible poses. Is it possible to automatically select the poses based on the position and orientation of one partner, for example, the ones in which the ligand protein is close to the transmembrane region of the receptor protein and oriented with its N-terminus on the extracellular side?
> 
> Thanks
> 
> Yu Zhou
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