How to determine the distance from SG of Cys to the centroid of a nearby Trp ring
I am using Tools/Structure Analysis/Axes -Planes-Centroids. Selecting the Trp Indole ring, obtaining the centroid. Then selecting SG of Cys and the centroid and drawing an axis. That axis does not seem to pass (exactly) through the SG and Centroid- that' my first problem, the 2nd problem is to get the distance between the centroid and SG.
Hi Ajay, I'm not sure how (or why) you are trying to draw an axis between an atom and a centroid: an axis is calculated from a set of atoms and it won't work to generate an axis from one atom and one centroid. If you are just trying to measure the distance, you only need select the SG atom (for example using Ctrl-click) and then click on the row for the centroid in the Axes/Planes/Centroids table and then the "Report distance" button in the same dialog. It will show the distance on the dialog and in the Reply Log. Or, you could use the "distance" command, for example between centroid with ID c1 (as shown in the table) and atom SG in Cys-25 of model 0 chain A: distance c1 #0:25.a@sg This will report the distance in the status line across the bottom of the Chimera window and in the reply log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> 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 Sep 12, 2013, at 1:52 PM, "Pande, Ajay K" <apande@albany.edu> wrote:
I am using Tools/Structure Analysis/Axes -Planes-Centroids. Selecting the Trp Indole ring, obtaining the centroid. Then selecting SG of Cys and the centroid and drawing an axis. That axis does not seem to pass (exactly) through the SG and Centroid- that' my first problem, the 2nd problem is to get the distance between the centroid and SG.
Hi Elaine Thanks for the information. But if I want the angle (and distance) from the centroid of a ring system (Trp or Phe , for example) to the SG of a Cys, how would I get that? Ajay ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, September 12, 2013 7:52 PM To: Pande, Ajay K Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] How to determine the distance from SG of Cys to the centroid of a nearby Trp ring Hi Ajay, I'm not sure how (or why) you are trying to draw an axis between an atom and a centroid: an axis is calculated from a set of atoms and it won't work to generate an axis from one atom and one centroid. If you are just trying to measure the distance, you only need select the SG atom (for example using Ctrl-click) and then click on the row for the centroid in the Axes/Planes/Centroids table and then the "Report distance" button in the same dialog. It will show the distance on the dialog and in the Reply Log. Or, you could use the "distance" command, for example between centroid with ID c1 (as shown in the table) and atom SG in Cys-25 of model 0 chain A: distance c1 #0:25.a@sg This will report the distance in the status line across the bottom of the Chimera window and in the reply log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> 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 Sep 12, 2013, at 1:52 PM, "Pande, Ajay K" <apande@albany.edu> wrote:
I am using Tools/Structure Analysis/Axes -Planes-Centroids. Selecting the Trp Indole ring, obtaining the centroid. Then selecting SG of Cys and the centroid and drawing an axis. That axis does not seem to pass (exactly) through the SG and Centroid- that' my first problem, the 2nd problem is to get the distance between the centroid and SG.
Hi Ajay, My previous message already described how to measure the distance between a centroid and an atom. There is no angle between two points (centroid and atom), only a line, but you probably meant the angle between such a line and the plane of the Trp or Phe ring. This is a little trickier and requires one manual calculation. Steps: (1) measure the centroid-atom distance, D1 (as described in the previous message) (2) use Axes/Planes/Centroids to define a plane from the ring atoms (3) measure the plane-atom distance, D2 (how to do it is the same as measuring the centroid-atom distance except you would choose or specify the plane instead of the centroid) (4) calculate the angle "manually" as arcsin(D2/D1) I hope this helps, Elaine On Sep 13, 2013, at 2:50 PM, Pande, Ajay K wrote:
Hi Elaine
Thanks for the information. But if I want the angle (and distance) from the centroid of a ring system (Trp or Phe , for example) to the SG of a Cys, how would I get that?
Ajay
________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, September 12, 2013 7:52 PM To: Pande, Ajay K Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] How to determine the distance from SG of Cys to the centroid of a nearby Trp ring
Hi Ajay, I'm not sure how (or why) you are trying to draw an axis between an atom and a centroid: an axis is calculated from a set of atoms and it won't work to generate an axis from one atom and one centroid.
If you are just trying to measure the distance, you only need select the SG atom (for example using Ctrl-click) and then click on the row for the centroid in the Axes/Planes/Centroids table and then the "Report distance" button in the same dialog. It will show the distance on the dialog and in the Reply Log. Or, you could use the "distance" command, for example between centroid with ID c1 (as shown in the table) and atom SG in Cys-25 of model 0 chain A:
distance c1 #0:25.a@sg
This will report the distance in the status line across the bottom of the Chimera window and in the reply log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
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 Sep 12, 2013, at 1:52 PM, "Pande, Ajay K" <apande@albany.edu> wrote:
I am using Tools/Structure Analysis/Axes -Planes-Centroids. Selecting the Trp Indole ring, obtaining the centroid. Then selecting SG of Cys and the centroid and drawing an axis. That axis does not seem to pass (exactly) through the SG and Centroid- that' my first problem, the 2nd problem is to get the distance between the centroid and SG.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Elaine, All that worked- thanks. Now, how do I show the line connecting the centroid to an atom (i.e.D1), which would also show its length in Angstroms? Thanks Ajay ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Friday, September 13, 2013 7:23 PM To: Pande, Ajay K Cc: chimera-users@cgl.ucsf.edu List Subject: Re: [Chimera-users] How to determine the distance from SG of Cys to the centroid of a nearby Trp ring Hi Ajay, My previous message already described how to measure the distance between a centroid and an atom. There is no angle between two points (centroid and atom), only a line, but you probably meant the angle between such a line and the plane of the Trp or Phe ring. This is a little trickier and requires one manual calculation. Steps: (1) measure the centroid-atom distance, D1 (as described in the previous message) (2) use Axes/Planes/Centroids to define a plane from the ring atoms (3) measure the plane-atom distance, D2 (how to do it is the same as measuring the centroid-atom distance except you would choose or specify the plane instead of the centroid) (4) calculate the angle "manually" as arcsin(D2/D1) I hope this helps, Elaine On Sep 13, 2013, at 2:50 PM, Pande, Ajay K wrote:
Hi Elaine
Thanks for the information. But if I want the angle (and distance) from the centroid of a ring system (Trp or Phe , for example) to the SG of a Cys, how would I get that?
Ajay
________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, September 12, 2013 7:52 PM To: Pande, Ajay K Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] How to determine the distance from SG of Cys to the centroid of a nearby Trp ring
Hi Ajay, I'm not sure how (or why) you are trying to draw an axis between an atom and a centroid: an axis is calculated from a set of atoms and it won't work to generate an axis from one atom and one centroid.
If you are just trying to measure the distance, you only need select the SG atom (for example using Ctrl-click) and then click on the row for the centroid in the Axes/Planes/Centroids table and then the "Report distance" button in the same dialog. It will show the distance on the dialog and in the Reply Log. Or, you could use the "distance" command, for example between centroid with ID c1 (as shown in the table) and atom SG in Cys-25 of model 0 chain A:
distance c1 #0:25.a@sg
This will report the distance in the status line across the bottom of the Chimera window and in the reply log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
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 Sep 12, 2013, at 1:52 PM, "Pande, Ajay K" <apande@albany.edu> wrote:
I am using Tools/Structure Analysis/Axes -Planes-Centroids. Selecting the Trp Indole ring, obtaining the centroid. Then selecting SG of Cys and the centroid and drawing an axis. That axis does not seem to pass (exactly) through the SG and Centroid- that' my first problem, the 2nd problem is to get the distance between the centroid and SG.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Ajay, Unfortunately there isn't any way to draw a line between a centroid and an atom. Instead you would need to add an atom at the centroid position, then measure atom-atom distance (which is shown as a line). You can add an atom at specified coordinates using Build Structure (in menu under Tools… Structure Editing), Start Structure section. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start> Centroid coordinates are reported in the Reply Log (under Favorites in menu) when the centroid is created, and can be written to a file using the Save button on the Axes/Planes/Centroids dialog. Best 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 Sep 16, 2013, at 6:44 AM, "Pande, Ajay K" <apande@albany.edu> wrote:
Thanks Elaine,
All that worked- thanks. Now, how do I show the line connecting the centroid to an atom (i.e.D1), which would also show its length in Angstroms?
Thanks
Ajay
Another way to mark the center of a ring is with the command "measure center". After selecting the ring atoms use measure center sel mark true radius 0.5 This places a marker (same as an atom) at the center and makes its radius 0.5. Then use that marker/atom to show and measure distance. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center Tom On Sep 16, 2013, at 10:20 AM, Elaine Meng > wrote:
Hi Ajay, Unfortunately there isn't any way to draw a line between a centroid and an atom. Instead you would need to add an atom at the centroid position, then measure atom-atom distance (which is shown as a line).
You can add an atom at specified coordinates using Build Structure (in menu under Tools… Structure Editing), Start Structure section. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start>
Centroid coordinates are reported in the Reply Log (under Favorites in menu) when the centroid is created, and can be written to a file using the Save button on the Axes/Planes/Centroids dialog.
Best 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 Sep 16, 2013, at 6:44 AM, "Pande, Ajay K" wrote:
Thanks Elaine,
All that worked- thanks. Now, how do I show the line connecting the centroid to an atom (i.e.D1), which would also show its length in Angstroms?
Thanks
Ajay
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Elaine. ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Monday, September 16, 2013 1:20 PM To: Pande, Ajay K Cc: chimera-users@cgl.ucsf.edu List Subject: Re: [Chimera-users] How to determine the distance from SG of Cys to the centroid of a nearby Trp ring Hi Ajay, Unfortunately there isn't any way to draw a line between a centroid and an atom. Instead you would need to add an atom at the centroid position, then measure atom-atom distance (which is shown as a line). You can add an atom at specified coordinates using Build Structure (in menu under Tools… Structure Editing), Start Structure section. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start> Centroid coordinates are reported in the Reply Log (under Favorites in menu) when the centroid is created, and can be written to a file using the Save button on the Axes/Planes/Centroids dialog. Best 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 Sep 16, 2013, at 6:44 AM, "Pande, Ajay K" <apande@albany.edu> wrote:
Thanks Elaine,
All that worked- thanks. Now, how do I show the line connecting the centroid to an atom (i.e.D1), which would also show its length in Angstroms?
Thanks
Ajay
participants (3)
-
Elaine Meng -
Pande, Ajay K -
Tom Goddard