[Chimera-users] measuring distance between an atom and centroid of an aromatic ring

[Aswani Kumar Kancherla]

Dear Elaine and Tom,

Many thanks for the prompt replies.

I could get both the methods to work. I measured the distances and
displayed them by creating pseudo-atoms at the coordinates of the centroid
as suggested by Elaine.  I pasted the figure below.

Many thanks for the wonderful program and support.

with regards,
Aswani


​

On 9 October 2014 05:55, Tom Goddard <goddard at sonic.net> wrote:

> Hello Aswani,
>
>   If you want to show the distance to the centroid of the ring, you can
> select the ring atoms (ctrl-click and shift-ctrl-click) then use
>
> measure center sel mark true radius .3
>
> This puts a marker (which is just like an atom) at the center of the
> ring.  Then to show the distance I ctrl-click the marker then
> shift-ctrl-double-click the atom I want to measure the distance too — that
> shows a menu and I choose “Show distance”.  Picture shows the result.  Here
> are the “measure center” docs.
>
>
> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#center
>
> There are usually lots of ways to do things in Chimera.
>
>   Tom
>
>
>
> On Oct 8, 2014, at 5:12 PM, Elaine Meng  wrote:
>
> Hello Aswani,
> It won’t draw a line like atom-atom distance measurements, but you can
> certainly get the values.  You can use the distance command to get a
> pairwise centroid-atom distance, for example:
>
> distance c1 #0:200.A at n
>
> (centroid with ID c1 to atom N in residue 200 chain A of model 0).  The
> centroid IDs are shown in the Axes/Planes/Centroids dialog.
>
> Or, you could select one atom and use command:
>
> distance c1 sel
>
> Or, to measure the distances from a centroid to multiple selected atoms,
> choose the row for the centroid in the Axes/Planes/Centroids dialog and
> then click the “Report distance” button.
>
> In all cases, the resulting distance values will be reported in the Reply
> Log (main menu Favorites… Reply Log).
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes
> >
>
> The centroid is actually a surface model and not an atom, which is why the
> behavior is different than with two atoms.  If you wanted to make a fake
> atom in the centroid position, it is a bit more bothersome.  To do that,
> you could use the “Save” button on Axes/Planes/Centroids to save the
> centroids information including their coordinates to a text file.  Then you
> could use Build Structure (in menu under Tools… Structure Editing), “Start
> Structure” and Add: “atom” with specified x,y,z coordinates copied from
> that file.  Then after you added the fake atom, you could use it for
> distance measurements the usual atom-atom way.
>
> 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 Oct 8, 2014, at 4:03 PM, Aswani Kumar Kancherla  wrote:
>
> Hello Chimera Users,
>
> I need to measure and mark the distances of a few atoms to the center of
> an aromatic ring.
>
> I could define and create a centroid and plane for the ring. However, I am
> unable to measure or mark the distances of the surrounding atoms from the
> centroid of the ring (This is an exercise to show the ring current effect
> of the aromatic ring on the chemical shifts of the neighboring protons).
>
> Could anyone please give a hint on how I can go about this?
>
> thanking you in advance,
> best wishes,
> Aswani
>
>
>
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>
>
>
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