Normal to the plane of the aromatic ring at the centroid
How would I draw a normal to the plane of an aromatic ring, at its centroid? Thanks Ajay Pande
On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" <apande@albany.edu> wrote:
How would I draw a normal to the plane of an aromatic ring, at its centroid?
Hi Ajay, There's not a 100% direct way in Chimera, but what you can do is this: 1) Define the plane of the aromatic ring using the Axes/Planes/Centroids tool. 2) Use that tool's Save button to save the plane info to a file. The info will include the plane center and normal. 3) Create a "BILD"-format file defining an arrow (BILD format here: BILD format). The start of the arrow would be at the center of the plane and the end (arrowhead) at the center plus some multiple of the normal. Since the normal is of length 1, maybe two or three times the normal would look okay. Also, the parameter that determines the width of the arrowhead should probably be reduced from the default value (4 times the arrow width) unless you make the arrow length considerably longer. Anyway, an example: .arrow 16.692 32.583 17.432 16.583 31.740 17.959 0.1 0.2 which shows a normal to the aromatic six-member ring of the ligand in PDB 121P. The plane info was: Planes plane name, center, normal, radius plane: ( 16.692, 32.583, 17.432) (-0.109, -0.843, 0.527) 1.446 3) Open the BILD file with the "open" or the File-Open menu item. Make sure the file name ends with ".bild". If the structure is the only other open model (or has the lowest model number), the arrow will be oriented correctly relative to the structure. Otherwise, you will either have to use an open command that also specifies that you want the BILD opened in the same model number as the structure (e.g. "open 5 myarrow.bild") or use the "transform as" button in the Model Panel to make the arrow have the same transformation matrix as the structure (which can also be accomplished with the matrixcopy command). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi Ajay, Ok, I have a totally twisted way to do this in Chimera. Select the ring atoms, say with the mouse (shift ctrl click each atom). Then measure inertia sel This shows an inertia ellipsoid centered on the atoms. Then how about just stretching the ellipsoid perpendicular to the plane and squeezing it in the plane to make a cigar? I thought I could do that with the sop transform command, but no such luck. So instead make a second inertia ellipsoid, rotate it, then show the rotation axis: measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #1 #2 color pink In the turn command I used the axis taken from the reply log given by the measure inertia command (v3, axis with largest inertia). Picture attached. Ok, this should be easier in Chimera! Tom On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote:
How would I draw a normal to the plane of an aromatic ring, at its centroid?
Thanks
Ajay Pande _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, I was in fact surprised that the operations you described actually worked - I did not comprehend what I was doing! But, my normal to the plane (cylinder) had a large unseemly diameter and too long a length. How can I control those? In the picture you attached, they look very nice. I also don't necessarily need the normal on both sides of the plane. Thanks Ajay ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 15, 2013 8:09 PM To: Pande, Ajay K Cc: chimera-users@cgl.ucsf.edu List Subject: Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid Hi Ajay, Ok, I have a totally twisted way to do this in Chimera. Select the ring atoms, say with the mouse (shift ctrl click each atom). Then measure inertia sel This shows an inertia ellipsoid centered on the atoms. Then how about just stretching the ellipsoid perpendicular to the plane and squeezing it in the plane to make a cigar? I thought I could do that with the sop transform command, but no such luck. So instead make a second inertia ellipsoid, rotate it, then show the rotation axis: measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #1 #2 color pink In the turn command I used the axis taken from the reply log given by the measure inertia command (v3, axis with largest inertia). Picture attached. Ok, this should be easier in Chimera! Tom [cid:4366A083-E964-4CE7-A651-B1F68AA4A781@cgl.ucsf.edu] On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote: How would I draw a normal to the plane of an aromatic ring, at its centroid? Thanks Ajay Pande _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Ajay, The example commands were if your molecule was model #0 and the two inertia ellipsoids were #1 and #2. But I see that if your molecule was #1 and the ellipsoids were #2 and #3 it still works but gives a fat long axis cylinder! You don't end up even using the second ellipsoid. The axis comes out fat and long because its size is based on the first model in the "measure rotation #1 #2" comand and that was your molecule model, instead of the much smaller ellipsoid model. As mentioned in the documentation on measure rotation it makes the axis length equal the size of the first model and the axis diameter equal 5% of that size. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation Now that you've discovered the second ellipsoid is not needed the axis can be made with measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #2 #1 color pink where we assume #1 is your molecule model and #2 is the inertia ellipsoid model. Substitute the correct model numbers for your case by checking the numbers in Model Panel (Favorites menu). And here's a better explanation of this bit of trickery. Measure inertia shows an ellipsoid surface that matches the inertia of the selected ring atoms and that surface is a new model. Then the turn command rotates the ellipsoid about the axis perpendicular to the ring with center being the center of the ellipsoid, and it rotates only the ellipsoid, not the molecule, and the axis is specified in the coordinate system of the ellipsoid, and we rotate 90 degrees (although an non-zero angle will work). Then the measure rotation command shows the rotation axis for one model that is rotated relative to another. Tom On Oct 16, 2013, at 3:31 AM, "Pande, Ajay K" wrote:
Hi Tom,
I was in fact surprised that the operations you described actually worked - I did not comprehend what I was doing!
But, my normal to the plane (cylinder) had a large unseemly diameter and too long a length. How can I control those? In the picture you attached, they look very nice. I also don't necessarily need the normal on both sides of the plane.
Thanks
Ajay
From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 15, 2013 8:09 PM To: Pande, Ajay K Cc: chimera-users@cgl.ucsf.edu List Subject: Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid
Hi Ajay,
Ok, I have a totally twisted way to do this in Chimera. Select the ring atoms, say with the mouse (shift ctrl click each atom). Then
measure inertia sel
This shows an inertia ellipsoid centered on the atoms. Then how about just stretching the ellipsoid perpendicular to the plane and squeezing it in the plane to make a cigar? I thought I could do that with the sop transform command, but no such luck. So instead make a second inertia ellipsoid, rotate it, then show the rotation axis:
measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #1 #2 color pink
In the turn command I used the axis taken from the reply log given by the measure inertia command (v3, axis with largest inertia). Picture attached. Ok, this should be easier in Chimera!
Tom
<1a0m_ring_axis.jpg>
On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote:
How would I draw a normal to the plane of an aromatic ring, at its centroid?
Thanks
Ajay Pande _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you very much. It worked beautifully!! Ajay ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Wednesday, October 16, 2013 1:03 PM To: Pande, Ajay K Cc: chimera-users@cgl.ucsf.edu List Subject: Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid Hi Ajay, The example commands were if your molecule was model #0 and the two inertia ellipsoids were #1 and #2. But I see that if your molecule was #1 and the ellipsoids were #2 and #3 it still works but gives a fat long axis cylinder! You don't end up even using the second ellipsoid. The axis comes out fat and long because its size is based on the first model in the "measure rotation #1 #2" comand and that was your molecule model, instead of the much smaller ellipsoid model. As mentioned in the documentation on measure rotation it makes the axis length equal the size of the first model and the axis diameter equal 5% of that size. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation Now that you've discovered the second ellipsoid is not needed the axis can be made with measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #2 #1 color pink where we assume #1 is your molecule model and #2 is the inertia ellipsoid model. Substitute the correct model numbers for your case by checking the numbers in Model Panel (Favorites menu). And here's a better explanation of this bit of trickery. Measure inertia shows an ellipsoid surface that matches the inertia of the selected ring atoms and that surface is a new model. Then the turn command rotates the ellipsoid about the axis perpendicular to the ring with center being the center of the ellipsoid, and it rotates only the ellipsoid, not the molecule, and the axis is specified in the coordinate system of the ellipsoid, and we rotate 90 degrees (although an non-zero angle will work). Then the measure rotation command shows the rotation axis for one model that is rotated relative to another. Tom On Oct 16, 2013, at 3:31 AM, "Pande, Ajay K" wrote: Hi Tom, I was in fact surprised that the operations you described actually worked - I did not comprehend what I was doing! But, my normal to the plane (cylinder) had a large unseemly diameter and too long a length. How can I control those? In the picture you attached, they look very nice. I also don't necessarily need the normal on both sides of the plane. Thanks Ajay ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, October 15, 2013 8:09 PM To: Pande, Ajay K Cc: chimera-users@cgl.ucsf.edu List Subject: Re: [Chimera-users] Normal to the plane of the aromatic ring at the centroid Hi Ajay, Ok, I have a totally twisted way to do this in Chimera. Select the ring atoms, say with the mouse (shift ctrl click each atom). Then measure inertia sel This shows an inertia ellipsoid centered on the atoms. Then how about just stretching the ellipsoid perpendicular to the plane and squeezing it in the plane to make a cigar? I thought I could do that with the sop transform command, but no such luck. So instead make a second inertia ellipsoid, rotate it, then show the rotation axis: measure inertia sel turn 0.428,0.497,0.755 90 center #2 model #2 coord #2 measure rotation #1 #2 color pink In the turn command I used the axis taken from the reply log given by the measure inertia command (v3, axis with largest inertia). Picture attached. Ok, this should be easier in Chimera! Tom <1a0m_ring_axis.jpg> On Oct 14, 2013, at 2:10 PM, "Pande, Ajay K" wrote: How would I draw a normal to the plane of an aromatic ring, at its centroid? Thanks Ajay Pande _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Eric Pettersen -
Pande, Ajay K -
Tom Goddard