Great Elaine, Many thanks. As always indebted. George

On 27 May 2016, at 20:02, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi George, You can define centroids and measure the distance between them, and define planes and measure the angle between them. You can do this for specific snapshots, or in MD Movie you can define a per-frame script and have it execute at every frame and report results to the Reply Log.

In my example data (PDB 1plx, NMR ensemble opened as trajectory from MD Movie), I tried this per-frame script (MD Movie menu: Per-Frame… Define script), Chimera commands:

echo frame: <FRAME> define centroid number 1 radius 0.5 :1@cg,cd1,cd2,ce1,ce2,cz define plane number 1 :1@cg,cd1,cd2,ce1,ce2,cz define centroid number 2 radius 0.5 :4@cg,cd1,cd2,ce1,ce2,cz define plane number 2 :4@cg,cd1,cd2,ce1,ce2,cz distance c1 c2 angle p1 p2

… which gave output like this in the Reply Log:

[…] frame: 09 centroid name, ID, center: centroid: c1 ( -2.594, 2.758, -1.103) plane name, ID, center, normal, radius: plane: p1 ( -2.594, 2.758, -1.103) ( 0.798, -0.576, -0.180) 1.399 centroid name, ID, center: centroid: c2 ( 2.361, -0.549, 1.599) plane name, ID, center, normal, radius: plane: p2 ( 2.361, -0.549, 1.599) (-0.725, 0.288, -0.626) 1.395 Distance from c1 to c2 is 6.541 Angle between p1 and p2 is 50.860 frame: 10 centroid name, ID, center: centroid: c1 ( -2.613, 3.441, -0.814) plane name, ID, center, normal, radius: plane: p1 ( -2.613, 3.441, -0.814) (-0.650, 0.693, 0.310) 1.399 centroid name, ID, center: centroid: c2 ( 1.560, -0.777, 1.955) plane name, ID, center, normal, radius: plane: p2 ( 1.560, -0.777, 1.955) (-0.749, 0.092, -0.657) 1.394 Distance from c1 to c2 is 6.548 Angle between p1 and p2 is 69.698 […]

You would give different residue numbers and atom names to define the centroids and planes in your own data, but otherwise it would be basically similar.

I also attached an image of my example system with the centroids and planes shown.

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

<1plx-image.png>

On May 27, 2016, at 1:30 AM, George Tzotzos <gtzotzos@me.com <mailto:gtzotzos@me.com>> wrote:

...

Having generated a 100ns trajectory, I’m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I’m dealing with pi-pi stacking interactions.

I’ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven’t managed to find a solution for measuring the angles between the two planes defined by the ring atoms.

I’d appreciate any suggestions on possible solutions to the problem described above. I’m attaching a snapshot of measuring distances between two atoms (not really a good solution).

Thanks in advance

George

<PastedGraphic-2.pdf>

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Hi George, You cannot show a dotted line between two centroids. Instead you would have to use different commands to make “markers” (fake atoms) instead of centroids. Then with the 2 markers you could use any of the same methods as you could use to show a distance between 2 atoms. Here are some example commands: measure center :1@cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color orange model #5 measure center :4@cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color plum model #6 distance #5 #6 … this just creates markers as new models #5 and #6, then draws a distance monitor between them. You would specify the sets of atoms as needed for your data, and for the markers, you can use any radius or color. You can also change the color, thickness, etc. of the distance pseudobond, e.g. Tools… Structure Analysis… Distances, then change “depiction options” within that dialog. Another difference to note between “measure center” and “define centroid” is that “measure center” always uses mass weighting, whereas with “define centroid” you have a choice of mass-weighting or not (default is not). In my example all the atoms are carbons, so it wouldn’t make a difference, but in other cases there may be small differences between the mass-weighted and non-mass-weighted centroid locations. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid> 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 9, 2016, at 7:15 AM, George Tzotzos <gtzotzos@me.com> wrote:

Hi Elaine,

Sorry to bother you again on the same subject.

As I mentioned earlier, your script worked just fine. At this point, and for one frame only, I’d like to generate an image showing the distance between the two centroids. I tried to do it by the pseudo bond command to no avail. I’m sure there’s a way to do this but I haven’t been able to work it out.

Any help would be most welcome.

Regards

George

...

On 27 May 2016, at 19:02, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi George, You can define centroids and measure the distance between them, and define planes and measure the angle between them. You can do this for specific snapshots, or in MD Movie you can define a per-frame script and have it execute at every frame and report results to the Reply Log.

In my example data (PDB 1plx, NMR ensemble opened as trajectory from MD Movie), I tried this per-frame script (MD Movie menu: Per-Frame… Define script), Chimera commands:

echo frame: <FRAME> define centroid number 1 radius 0.5 :1@cg,cd1,cd2,ce1,ce2,cz define plane number 1 :1@cg,cd1,cd2,ce1,ce2,cz define centroid number 2 radius 0.5 :4@cg,cd1,cd2,ce1,ce2,cz define plane number 2 :4@cg,cd1,cd2,ce1,ce2,cz distance c1 c2 angle p1 p2

… which gave output like this in the Reply Log:

[…] frame: 09 centroid name, ID, center: centroid: c1 ( -2.594, 2.758, -1.103) plane name, ID, center, normal, radius: plane: p1 ( -2.594, 2.758, -1.103) ( 0.798, -0.576, -0.180) 1.399 centroid name, ID, center: centroid: c2 ( 2.361, -0.549, 1.599) plane name, ID, center, normal, radius: plane: p2 ( 2.361, -0.549, 1.599) (-0.725, 0.288, -0.626) 1.395 Distance from c1 to c2 is 6.541 Angle between p1 and p2 is 50.860 frame: 10 centroid name, ID, center: centroid: c1 ( -2.613, 3.441, -0.814) plane name, ID, center, normal, radius: plane: p1 ( -2.613, 3.441, -0.814) (-0.650, 0.693, 0.310) 1.399 centroid name, ID, center: centroid: c2 ( 1.560, -0.777, 1.955) plane name, ID, center, normal, radius: plane: p2 ( 1.560, -0.777, 1.955) (-0.749, 0.092, -0.657) 1.394 Distance from c1 to c2 is 6.548 Angle between p1 and p2 is 69.698 […]

You would give different residue numbers and atom names to define the centroids and planes in your own data, but otherwise it would be basically similar.

I also attached an image of my example system with the centroids and planes shown.

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

<1plx-image.png>

On May 27, 2016, at 1:30 AM, George Tzotzos <gtzotzos@me.com> wrote:

...

Having generated a 100ns trajectory, I’m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I’m dealing with pi-pi stacking interactions.

I’ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven’t managed to find a solution for measuring the angles between the two planes defined by the ring atoms.

I’d appreciate any suggestions on possible solutions to the problem described above. I’m attaching a snapshot of measuring distances between two atoms (not really a good solution).

Thanks in advance

George

<PastedGraphic-2.pdf>

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Hi Elaine, I’m writing as a follow up of our earlier exchange of emails (see below). I followed your suggestion and I generated the requisite “markers”. Model # 6 corresponds to marker of Phe123. Model #5 corresponds to the marker of the ligand. distance #5 #6 throws the following error “Exactly two atoms/axes/planes must be selected. You selected 6”. See attached snapshot. When I select #6, I get “1 atom selected”. When I select #5, I get “5 atoms selected”. Any help on this one would be most welcome. Best regards George

On 09 Jun 2016, at 18:13, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi George, You cannot show a dotted line between two centroids. Instead you would have to use different commands to make “markers” (fake atoms) instead of centroids. Then with the 2 markers you could use any of the same methods as you could use to show a distance between 2 atoms.

Here are some example commands:

measure center :1@cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color orange model #5 measure center :4@cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color plum model #6 distance #5 #6

… this just creates markers as new models #5 and #6, then draws a distance monitor between them. You would specify the sets of atoms as needed for your data, and for the markers, you can use any radius or color. You can also change the color, thickness, etc. of the distance pseudobond, e.g. Tools… Structure Analysis… Distances, then change “depiction options” within that dialog.

Another difference to note between “measure center” and “define centroid” is that “measure center” always uses mass weighting, whereas with “define centroid” you have a choice of mass-weighting or not (default is not). In my example all the atoms are carbons, so it wouldn’t make a difference, but in other cases there may be small differences between the mass-weighted and non-mass-weighted centroid locations.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid>

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 9, 2016, at 7:15 AM, George Tzotzos <gtzotzos@me.com> wrote:

Hi Elaine,

Sorry to bother you again on the same subject.

As I mentioned earlier, your script worked just fine. At this point, and for one frame only, I’d like to generate an image showing the distance between the two centroids. I tried to do it by the pseudo bond command to no avail. I’m sure there’s a way to do this but I haven’t been able to work it out.

Any help would be most welcome.

Regards

George

...

On 27 May 2016, at 19:02, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi George, You can define centroids and measure the distance between them, and define planes and measure the angle between them. You can do this for specific snapshots, or in MD Movie you can define a per-frame script and have it execute at every frame and report results to the Reply Log.

In my example data (PDB 1plx, NMR ensemble opened as trajectory from MD Movie), I tried this per-frame script (MD Movie menu: Per-Frame… Define script), Chimera commands:

echo frame: <FRAME> define centroid number 1 radius 0.5 :1@cg,cd1,cd2,ce1,ce2,cz define plane number 1 :1@cg,cd1,cd2,ce1,ce2,cz define centroid number 2 radius 0.5 :4@cg,cd1,cd2,ce1,ce2,cz define plane number 2 :4@cg,cd1,cd2,ce1,ce2,cz distance c1 c2 angle p1 p2

… which gave output like this in the Reply Log:

[…] frame: 09 centroid name, ID, center: centroid: c1 ( -2.594, 2.758, -1.103) plane name, ID, center, normal, radius: plane: p1 ( -2.594, 2.758, -1.103) ( 0.798, -0.576, -0.180) 1.399 centroid name, ID, center: centroid: c2 ( 2.361, -0.549, 1.599) plane name, ID, center, normal, radius: plane: p2 ( 2.361, -0.549, 1.599) (-0.725, 0.288, -0.626) 1.395 Distance from c1 to c2 is 6.541 Angle between p1 and p2 is 50.860 frame: 10 centroid name, ID, center: centroid: c1 ( -2.613, 3.441, -0.814) plane name, ID, center, normal, radius: plane: p1 ( -2.613, 3.441, -0.814) (-0.650, 0.693, 0.310) 1.399 centroid name, ID, center: centroid: c2 ( 1.560, -0.777, 1.955) plane name, ID, center, normal, radius: plane: p2 ( 1.560, -0.777, 1.955) (-0.749, 0.092, -0.657) 1.394 Distance from c1 to c2 is 6.548 Angle between p1 and p2 is 69.698 […]

You would give different residue numbers and atom names to define the centroids and planes in your own data, but otherwise it would be basically similar.

I also attached an image of my example system with the centroids and planes shown.

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

<1plx-image.png>

On May 27, 2016, at 1:30 AM, George Tzotzos <gtzotzos@me.com> wrote:

...

Having generated a 100ns trajectory, I’m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I’m dealing with pi-pi stacking interactions.

I’ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven’t managed to find a solution for measuring the angles between the two planes defined by the ring atoms.

I’d appreciate any suggestions on possible solutions to the problem described above. I’m attaching a snapshot of measuring distances between two atoms (not really a good solution).

Thanks in advance

George

<PastedGraphic-2.pdf>

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Thank you Elaine, I don’t know how I goofed in the first place but with your help the problem is resolved. All the best George

On 26 Sep 2016, at 20:47, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi George, I can only guess that maybe you accidentally made 5 ligand markers in the same place. You could try closing #5 and then starting over to make the ligand marker, being careful to make it only once. I hope this helps, Elaine

...

On Sep 26, 2016, at 9:49 AM, George Tzotzos <gtzotzos@me.com> wrote:

Hi Elaine,

I’m writing as a follow up of our earlier exchange of emails (see below). I followed your suggestion and I generated the requisite “markers”.

Model # 6 corresponds to marker of Phe123. Model #5 corresponds to the marker of the ligand.

distance #5 #6 throws the following error “Exactly two atoms/axes/planes must be selected. You selected 6”. See attached snapshot.

When I select #6, I get “1 atom selected”. When I select #5, I get “5 atoms selected”.

Any help on this one would be most welcome.

Best regards

George

<PastedGraphic-1.tiff>

...

On 09 Jun 2016, at 18:13, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi George, You cannot show a dotted line between two centroids. Instead you would have to use different commands to make “markers” (fake atoms) instead of centroids. Then with the 2 markers you could use any of the same methods as you could use to show a distance between 2 atoms.

Here are some example commands:

measure center :1@cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color orange model #5 measure center :4@cg,cd1,cd2,ce1,ce2,cz mark true radius 0.5 color plum model #6 distance #5 #6

… this just creates markers as new models #5 and #6, then draws a distance monitor between them. You would specify the sets of atoms as needed for your data, and for the markers, you can use any radius or color. You can also change the color, thickness, etc. of the distance pseudobond, e.g. Tools… Structure Analysis… Distances, then change “depiction options” within that dialog.

Another difference to note between “measure center” and “define centroid” is that “measure center” always uses mass weighting, whereas with “define centroid” you have a choice of mass-weighting or not (default is not). In my example all the atoms are carbons, so it wouldn’t make a difference, but in other cases there may be small differences between the mass-weighted and non-mass-weighted centroid locations.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid>

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 9, 2016, at 7:15 AM, George Tzotzos <gtzotzos@me.com> wrote:

Hi Elaine,

Sorry to bother you again on the same subject.

As I mentioned earlier, your script worked just fine. At this point, and for one frame only, I’d like to generate an image showing the distance between the two centroids. I tried to do it by the pseudo bond command to no avail. I’m sure there’s a way to do this but I haven’t been able to work it out.

Any help would be most welcome.

Regards

George

...

On 27 May 2016, at 19:02, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi George, You can define centroids and measure the distance between them, and define planes and measure the angle between them. You can do this for specific snapshots, or in MD Movie you can define a per-frame script and have it execute at every frame and report results to the Reply Log.

In my example data (PDB 1plx, NMR ensemble opened as trajectory from MD Movie), I tried this per-frame script (MD Movie menu: Per-Frame… Define script), Chimera commands:

echo frame: <FRAME> define centroid number 1 radius 0.5 :1@cg,cd1,cd2,ce1,ce2,cz define plane number 1 :1@cg,cd1,cd2,ce1,ce2,cz define centroid number 2 radius 0.5 :4@cg,cd1,cd2,ce1,ce2,cz define plane number 2 :4@cg,cd1,cd2,ce1,ce2,cz distance c1 c2 angle p1 p2

… which gave output like this in the Reply Log:

[…] frame: 09 centroid name, ID, center: centroid: c1 ( -2.594, 2.758, -1.103) plane name, ID, center, normal, radius: plane: p1 ( -2.594, 2.758, -1.103) ( 0.798, -0.576, -0.180) 1.399 centroid name, ID, center: centroid: c2 ( 2.361, -0.549, 1.599) plane name, ID, center, normal, radius: plane: p2 ( 2.361, -0.549, 1.599) (-0.725, 0.288, -0.626) 1.395 Distance from c1 to c2 is 6.541 Angle between p1 and p2 is 50.860 frame: 10 centroid name, ID, center: centroid: c1 ( -2.613, 3.441, -0.814) plane name, ID, center, normal, radius: plane: p1 ( -2.613, 3.441, -0.814) (-0.650, 0.693, 0.310) 1.399 centroid name, ID, center: centroid: c2 ( 1.560, -0.777, 1.955) plane name, ID, center, normal, radius: plane: p2 ( 1.560, -0.777, 1.955) (-0.749, 0.092, -0.657) 1.394 Distance from c1 to c2 is 6.548 Angle between p1 and p2 is 69.698 […]

You would give different residue numbers and atom names to define the centroids and planes in your own data, but otherwise it would be basically similar.

I also attached an image of my example system with the centroids and planes shown.

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

<1plx-image.png>

On May 27, 2016, at 1:30 AM, George Tzotzos <gtzotzos@me.com> wrote:

...

Having generated a 100ns trajectory, I’m interested in measuring the time evolution of the distance between to aromatic ring centroids as well as the angle between the planes of these two rings. The idea is to determine if I’m dealing with pi-pi stacking interactions.

I’ve check past correspondence and tried various permutations of commands to no avail. Maybe my best option is to do this for selected snapshots and define for each snapshot two centroids (e.g. c1 and c2) and measure the distance c1 c2. I haven’t managed to find a solution for measuring the angles between the two planes defined by the ring atoms.

I’d appreciate any suggestions on possible solutions to the problem described above. I’m attaching a snapshot of measuring distances between two atoms (not really a good solution).

Thanks in advance

George

<PastedGraphic-2.pdf>

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users