[Chimera-users] defining planes and finding nearby atoms

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 29 11:26:55 PDT 2016


Hi Allessandra,
Sorry, there is no way to automatically find atoms that are close to a plane.  It would require scripting (“define” command to create planes, “distance” to measure distance between each atom and a specific plane, python to loop over all atoms and to select only the ones with short distances).  Distance measurements are also reported in the Reply Log and could be saved from there.  You can save the set of selected atoms to a file (menu: File… Save PDB or command “write” with the option to save only selected atoms).

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

The planes are not all the same.  Each will have a different size, orientation, and location because it is simply derived from the coordinates of the atoms used to define it.  

There is one way that might work to superimpose the structures using their individual planes, but I don’t know how well it would work (so maybe you should just skip to the next paragraph):  use “align” commands to position each structure with its plane in the middle of the window facing the viewer, and then because some of them will be facing the wrong way (no way to distinguish the two sides of the plane), flip them using “turn y 180 center view” plus the “models” option to specify only the ones that need flipping.  It would probably take a few separate attempts because you should not move anything with the mouse until after all of the align and turn commands.  So the first time I’d just use all the align commands, one for each plane/structure, and then use the mouse to see which ones need flipping, and then I’d repeat all the align commands followed by turn as needed.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/align.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>

However, instead of trying to superimpose the individual planes, it may work better to first superimpose all your structures and then define a single master plane. 

I hope this helps,
Elaine
-----
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 7:43 AM, Alessandra Gastaldello <Alessandra.Gastaldello at sib.swiss> wrote:

> Thank you again Elaine! Very very useful.
> Unfortunately, I have another question.
> I would like to define a plane using the coordinates of some atoms in a structure and then to calculate the coordinates of the atoms that "surround" that plane. I know there is the "define plane" function to do that.
> But how can I get the coordinates of all atoms around that plane?
> 
> Moreover I would like to compare that coordinates with the coordinates of other atoms in other structures calculated in the same way (defining a plane).
> In summary, I would like to see the atom distribution around some atom positions in different structures and to compare it.
> This means I would have to have a same "reference" plane for all atoms even if they are in different structures.
> 
> Can I consider the different planes defined in the different structures as identical planes?
> I mean, is each of them as an "origin" plane, spatially identical to other calculated in the same way?
> Can I compare the coordinates of all the atoms in the different structures ?
> Or should I define a big unique plane specifying coordinates from all the structures and after calculate the distance of the atoms from that unique plane?
> 
> Thank you very much in advance!
> 
> -- 
> Alessandra Gastaldello




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