measuring distance between an atom and centroid of an aromatic ring
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 -- K.Aswani Kumar Graduate Student Molecular Biophysics Unit Indian Institute of Science Bangalore-560012 Karnataka, India.
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@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 <ashwin2952@gmail.com> 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
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#c... 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@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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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#c...
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@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/stru...
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Aswani Kumar Kancherla -
Elaine Meng -
Tom Goddard