Hi Oliver, If you have a plane defined in Axes/Planes/Centroids, you can write out its information including the normal (Save button on that tool), then place atoms at either end allowing you to define the axis. There are a few steps... In my little test, the plane output information included: Planes plane name, ID, center, normal, radius plane: p1 ( 19.023, 17.733, 7.080) (-0.380, 0.757, 0.531) 24.199 Then I used Tools… Build Structure, Start Structure, add atom at specific coordinates to add two atoms, one at the center of that plane and one to show the normal. The latter's coordinates are (center + normal) coordinates, and you can multiply the normal coordinates by some constant to make the axis longer. For example, I multiplied the normal coordinates by 10 before adding them to the center coordinates to give the position of the second atom as: x 15.223 y 25.303 z 12.390 Then I selected the two new atoms and used them to define an axis in Axes/Planes/Centroids, see attached image. 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 Apr 6, 2015, at 5:01 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Alternatively, would it be possible (or is there some way already) to define a separate axis that is the normal of a plane? In this case I’m working with an ion channel, so I’m looking for a consistent way to represent the change in orientation of particular extramembrane domains with respect to the channel axis. If I could define an axis for the membrane plane normal, I could at least measure the absolute orientation of the principal axes of particular domains or individual helices with respect to the channel axis. It seems like the plane normal is computed already (because there is an option in axes/planes/centroids) to align screen x/y/z to it, but I can’t see a way to generate it as a separate axis that I can use for measuring angles etc.
Thanks for all your help as always!
Oliver.
Thanks Elaine, that’s very helpful indeed. The other way I figured out was to define two centroids using a single atom from each subunit in the channel from two sets of residues in different planes (which would otherwise define two parallel planes) and define an axis from the two resultant centroids. Your way looks more general though - I will see if I can figure out a way to put it into an alias so I can call it with a single command. Best, Oliver.
On Apr 7, 2015, at 1:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, If you have a plane defined in Axes/Planes/Centroids, you can write out its information including the normal (Save button on that tool), then place atoms at either end allowing you to define the axis. There are a few steps...
In my little test, the plane output information included:
Planes plane name, ID, center, normal, radius plane: p1 ( 19.023, 17.733, 7.080) (-0.380, 0.757, 0.531) 24.199
Then I used Tools… Build Structure, Start Structure, add atom at specific coordinates to add two atoms, one at the center of that plane and one to show the normal. The latter's coordinates are (center + normal) coordinates, and you can multiply the normal coordinates by some constant to make the axis longer. For example, I multiplied the normal coordinates by 10 before adding them to the center coordinates to give the position of the second atom as:
x 15.223 y 25.303 z 12.390
Then I selected the two new atoms and used them to define an axis in Axes/Planes/Centroids, see attached image. 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
<junk.png>
On Apr 6, 2015, at 5:01 PM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
Alternatively, would it be possible (or is there some way already) to define a separate axis that is the normal of a plane? In this case I’m working with an ion channel, so I’m looking for a consistent way to represent the change in orientation of particular extramembrane domains with respect to the channel axis. If I could define an axis for the membrane plane normal, I could at least measure the absolute orientation of the principal axes of particular domains or individual helices with respect to the channel axis. It seems like the plane normal is computed already (because there is an option in axes/planes/centroids) to align screen x/y/z to it, but I can’t see a way to generate it as a separate axis that I can use for measuring angles etc.
Thanks for all your help as always!
Oliver.
My way would definitely require python, to calculate coordinates for the second atom and to create the atoms (there's no Chimera command for that). Your way might be possible to make into an alias, since you can use the "define" command. Elaine On Apr 7, 2015, at 11:32 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Thanks Elaine, that’s very helpful indeed. The other way I figured out was to define two centroids using a single atom from each subunit in the channel from two sets of residues in different planes (which would otherwise define two parallel planes) and define an axis from the two resultant centroids. Your way looks more general though - I will see if I can figure out a way to put it into an alias so I can call it with a single command.
Best, Oliver.
On Apr 7, 2015, at 1:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, If you have a plane defined in Axes/Planes/Centroids, you can write out its information including the normal (Save button on that tool), then place atoms at either end allowing you to define the axis. There are a few steps...
In my little test, the plane output information included:
Planes plane name, ID, center, normal, radius plane: p1 ( 19.023, 17.733, 7.080) (-0.380, 0.757, 0.531) 24.199
Then I used Tools… Build Structure, Start Structure, add atom at specific coordinates to add two atoms, one at the center of that plane and one to show the normal. The latter's coordinates are (center + normal) coordinates, and you can multiply the normal coordinates by some constant to make the axis longer. For example, I multiplied the normal coordinates by 10 before adding them to the center coordinates to give the position of the second atom as:
x 15.223 y 25.303 z 12.390
Then I selected the two new atoms and used them to define an axis in Axes/Planes/Centroids, see attached image. 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
<junk.png>
On Apr 6, 2015, at 5:01 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Alternatively, would it be possible (or is there some way already) to define a separate axis that is the normal of a plane? In this case I’m working with an ion channel, so I’m looking for a consistent way to represent the change in orientation of particular extramembrane domains with respect to the channel axis. If I could define an axis for the membrane plane normal, I could at least measure the absolute orientation of the principal axes of particular domains or individual helices with respect to the channel axis. It seems like the plane normal is computed already (because there is an option in axes/planes/centroids) to align screen x/y/z to it, but I can’t see a way to generate it as a separate axis that I can use for measuring angles etc.
Thanks for all your help as always!
Oliver.
So I enhanced the "define axis" command so that if your atom spec is just a single plane identifier, it will create an axis normal to the plane. You have no control over the length of the axis, but I hope I've picked a reasonable default (1/2 the plane radius) and since you really want it for measurement purposes hopefully it doesn't really matter too much. Available in tonight's daily build. It will be awhile before I add the corresponding capability to the graphical interface. --Eric On Apr 7, 2015, at 11:32 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Thanks Elaine, that’s very helpful indeed. The other way I figured out was to define two centroids using a single atom from each subunit in the channel from two sets of residues in different planes (which would otherwise define two parallel planes) and define an axis from the two resultant centroids. Your way looks more general though - I will see if I can figure out a way to put it into an alias so I can call it with a single command.
Best, Oliver.
On Apr 7, 2015, at 1:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, If you have a plane defined in Axes/Planes/Centroids, you can write out its information including the normal (Save button on that tool), then place atoms at either end allowing you to define the axis. There are a few steps...
In my little test, the plane output information included:
Planes plane name, ID, center, normal, radius plane: p1 ( 19.023, 17.733, 7.080) (-0.380, 0.757, 0.531) 24.199
Then I used Tools… Build Structure, Start Structure, add atom at specific coordinates to add two atoms, one at the center of that plane and one to show the normal. The latter's coordinates are (center + normal) coordinates, and you can multiply the normal coordinates by some constant to make the axis longer. For example, I multiplied the normal coordinates by 10 before adding them to the center coordinates to give the position of the second atom as:
x 15.223 y 25.303 z 12.390
Then I selected the two new atoms and used them to define an axis in Axes/Planes/Centroids, see attached image. 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
<junk.png>
On Apr 6, 2015, at 5:01 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Alternatively, would it be possible (or is there some way already) to define a separate axis that is the normal of a plane? In this case I’m working with an ion channel, so I’m looking for a consistent way to represent the change in orientation of particular extramembrane domains with respect to the channel axis. If I could define an axis for the membrane plane normal, I could at least measure the absolute orientation of the principal axes of particular domains or individual helices with respect to the channel axis. It seems like the plane normal is computed already (because there is an option in axes/planes/centroids) to align screen x/y/z to it, but I can’t see a way to generate it as a separate axis that I can use for measuring angles etc.
Thanks for all your help as always!
Oliver.
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Great, thanks Eric! That is exactly what I was looking for, and you are correct in assuming that length doesn’t matter - angles between axes are what I’m after. Cheers, Oliver.
On Apr 7, 2015, at 7:20 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
So I enhanced the "define axis" command so that if your atom spec is just a single plane identifier, it will create an axis normal to the plane. You have no control over the length of the axis, but I hope I've picked a reasonable default (1/2 the plane radius) and since you really want it for measurement purposes hopefully it doesn't really matter too much. Available in tonight's daily build.
It will be awhile before I add the corresponding capability to the graphical interface.
--Eric
On Apr 7, 2015, at 11:32 AM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
Thanks Elaine, that’s very helpful indeed. The other way I figured out was to define two centroids using a single atom from each subunit in the channel from two sets of residues in different planes (which would otherwise define two parallel planes) and define an axis from the two resultant centroids. Your way looks more general though - I will see if I can figure out a way to put it into an alias so I can call it with a single command.
Best, Oliver.
On Apr 7, 2015, at 1:09 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hi Oliver, If you have a plane defined in Axes/Planes/Centroids, you can write out its information including the normal (Save button on that tool), then place atoms at either end allowing you to define the axis. There are a few steps...
In my little test, the plane output information included:
Planes plane name, ID, center, normal, radius plane: p1 ( 19.023, 17.733, 7.080) (-0.380, 0.757, 0.531) 24.199
Then I used Tools… Build Structure, Start Structure, add atom at specific coordinates to add two atoms, one at the center of that plane and one to show the normal. The latter's coordinates are (center + normal) coordinates, and you can multiply the normal coordinates by some constant to make the axis longer. For example, I multiplied the normal coordinates by 10 before adding them to the center coordinates to give the position of the second atom as:
x 15.223 y 25.303 z 12.390
Then I selected the two new atoms and used them to define an axis in Axes/Planes/Centroids, see attached image. 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
<junk.png>
On Apr 6, 2015, at 5:01 PM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
Alternatively, would it be possible (or is there some way already) to define a separate axis that is the normal of a plane? In this case I’m working with an ion channel, so I’m looking for a consistent way to represent the change in orientation of particular extramembrane domains with respect to the channel axis. If I could define an axis for the membrane plane normal, I could at least measure the absolute orientation of the principal axes of particular domains or individual helices with respect to the channel axis. It seems like the plane normal is computed already (because there is an option in axes/planes/centroids) to align screen x/y/z to it, but I can’t see a way to generate it as a separate axis that I can use for measuring angles etc.
Thanks for all your help as always!
Oliver.
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Oliver Clarke