measure rotation showAxis does not create a measurable object
Hello again, I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes. Two of my axes are #4 and #5. When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)" I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related. Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable? Cheers, Alexis
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper. That's not to disregard your suggestion, which makes sense. However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
Hi Alexis, Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model. Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
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Thanks Elaine, Indeed, the workaround works fine: I can use "defined axis #4" and "define axis #5" and then "angle #4.1 #5.1". What I find confusing is that if I do "defined axis #4 name foo" and "define axis #5 bar", then "angle foo bar" doesn't work. I guess "foo" and "bar" are not names of selections like I'm used to. Anyway, I think I've got what I need working now. And thanks Tom, your explanation makes sense. You wouldn't want to break existing use cases. Cheers, Alexis On Thu, Nov 16, 2023 at 5:35 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Alexis, Yeah the plain model name can't be used in lieu of a model specifier. You can use ##name=foo, which may not be that great for interactive use but might be handy if you were writing a script. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 17, 2023, at 8:31 AM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks Elaine,
Indeed, the workaround works fine: I can use "defined axis #4" and "define axis #5" and then "angle #4.1 #5.1".
What I find confusing is that if I do "defined axis #4 name foo" and "define axis #5 bar", then "angle foo bar" doesn't work. I guess "foo" and "bar" are not names of selections like I'm used to.
Anyway, I think I've got what I need working now.
And thanks Tom, your explanation makes sense. You wouldn't want to break existing use cases.
Cheers, Alexis
On Thu, Nov 16, 2023 at 5:35 PM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote: Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
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Hi Alexis, The "name" option of "define" gives the model name as shown in the Model Panel (not a named selection), as described here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html#options> E.g. if you open PDB 2gbp the model name is 2gbp but you can't use that in commands. You can use the separate "name" command to create a named selection that can be used in the command line: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Best, Elaine
On Nov 17, 2023, at 8:31 AM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks Elaine,
Indeed, the workaround works fine: I can use "defined axis #4" and "define axis #5" and then "angle #4.1 #5.1".
What I find confusing is that if I do "defined axis #4 name foo" and "define axis #5 bar", then "angle foo bar" doesn't work. I guess "foo" and "bar" are not names of selections like I'm used to.
Anyway, I think I've got what I need working now.
And thanks Tom, your explanation makes sense. You wouldn't want to break existing use cases.
Cheers, Alexis
On Thu, Nov 16, 2023 at 5:35 PM Tom Goddard <goddard@sonic.net> wrote: Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
Hi Alexis, I made the "angle" command handle the measure rotation axes, so if you have two axes #3 and #4 you can just use angle #3,4 As Elaine mentioned each axis is just a pair of atoms and now the angle command can take 4 atoms defining two vectors. We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it). Tom
On Nov 16, 2023, at 5:35 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Thanks Tom, that's great. We are also talking about adding an option to the measure rotation command
to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
I can see why you'd be ambivalent about this. The fact that it's easy to define an axis from the pair of atoms that is currently output means there's a really quick workaround anyway. Cheers, Alexis On Fri, Nov 17, 2023 at 11:35 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
I made the "angle" command handle the measure rotation axes, so if you have two axes #3 and #4 you can just use
angle #3,4
As Elaine mentioned each axis is just a pair of atoms and now the angle command can take 4 atoms defining two vectors. We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
Tom
On Nov 16, 2023, at 5:35 PM, Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
< https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Hi Alexis, I added an “axisType” keyword to “measure rotation” that accepts either ‘markers’ or ‘object’ as its value. So if you use the latter value you can create an axis object directly. The default is still “markers” for backwards compatibility. This change will be in the next daily build. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 17, 2023, at 12:56 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks Tom, that's great.
We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
I can see why you'd be ambivalent about this. The fact that it's easy to define an axis from the pair of atoms that is currently output means there's a really quick workaround anyway.
Cheers, Alexis
On Fri, Nov 17, 2023 at 11:35 AM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Alexis,
I made the "angle" command handle the measure rotation axes, so if you have two axes #3 and #4 you can just use
angle #3,4
As Elaine mentioned each axis is just a pair of atoms and now the angle command can take 4 atoms defining two vectors. We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
Tom
On Nov 16, 2023, at 5:35 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Excellent, thanks! By the way, for this and other changes made before the actual 1.7 release, will these features end up in 1.7? On Mon, Nov 20, 2023 at 11:04 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Alexis, I added an “axisType” keyword to “measure rotation” that accepts either ‘markers’ or ‘object’ as its value. So if you use the latter value you can create an axis object directly. The default is still “markers” for backwards compatibility. This change will be in the next daily build.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 17, 2023, at 12:56 PM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Thanks Tom, that's great.
We are also talking about adding an option to the measure rotation command
to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
I can see why you'd be ambivalent about this. The fact that it's easy to define an axis from the pair of atoms that is currently output means there's a really quick workaround anyway.
Cheers, Alexis
On Fri, Nov 17, 2023 at 11:35 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
I made the "angle" command handle the measure rotation axes, so if you have two axes #3 and #4 you can just use
angle #3,4
As Elaine mentioned each axis is just a pair of atoms and now the angle command can take 4 atoms defining two vectors. We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
Tom
On Nov 16, 2023, at 5:35 PM, Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
< https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
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In general, when we are in the candidate release stage, unless the developer says it is in both the upcoming release and daily, it is only in the daily. Once the release branch exists, one would have to specifically copy the development changes to the release branch as well, and we try to limit feature changes on the latter while it's in the shakeout period. Eric will have to weigh on this one specifically, however. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2023, at 11:56 AM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Excellent, thanks!
By the way, for this and other changes made before the actual 1.7 release, will these features end up in 1.7?
On Mon, Nov 20, 2023 at 11:04 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Alexis, I added an “axisType” keyword to “measure rotation” that accepts either ‘markers’ or ‘object’ as its value. So if you use the latter value you can create an axis object directly. The default is still “markers” for backwards compatibility. This change will be in the next daily build.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 17, 2023, at 12:56 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks Tom, that's great.
We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
I can see why you'd be ambivalent about this. The fact that it's easy to define an axis from the pair of atoms that is currently output means there's a really quick workaround anyway.
Cheers, Alexis
On Fri, Nov 17, 2023 at 11:35 AM Tom Goddard <goddard@sonic.net> wrote: Hi Alexis,
I made the "angle" command handle the measure rotation axes, so if you have two axes #3 and #4 you can just use
angle #3,4
As Elaine mentioned each axis is just a pair of atoms and now the angle command can take 4 atoms defining two vectors. We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
Tom
On Nov 16, 2023, at 5:35 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
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Yes, it will only be in the daily build, not the release candidate. —Eric
On Nov 20, 2023, at 12:05 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
In general, when we are in the candidate release stage, unless the developer says it is in both the upcoming release and daily, it is only in the daily. Once the release branch exists, one would have to specifically copy the development changes to the release branch as well, and we try to limit feature changes on the latter while it's in the shakeout period.
Eric will have to weigh on this one specifically, however.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2023, at 11:56 AM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Excellent, thanks!
By the way, for this and other changes made before the actual 1.7 release, will these features end up in 1.7?
On Mon, Nov 20, 2023 at 11:04 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Alexis, I added an “axisType” keyword to “measure rotation” that accepts either ‘markers’ or ‘object’ as its value. So if you use the latter value you can create an axis object directly. The default is still “markers” for backwards compatibility. This change will be in the next daily build.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 17, 2023, at 12:56 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thanks Tom, that's great.
We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
I can see why you'd be ambivalent about this. The fact that it's easy to define an axis from the pair of atoms that is currently output means there's a really quick workaround anyway.
Cheers, Alexis
On Fri, Nov 17, 2023 at 11:35 AM Tom Goddard <goddard@sonic.net> wrote: Hi Alexis,
I made the "angle" command handle the measure rotation axes, so if you have two axes #3 and #4 you can just use
angle #3,4
As Elaine mentioned each axis is just a pair of atoms and now the angle command can take 4 atoms defining two vectors. We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
Tom
On Nov 16, 2023, at 5:35 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello again,
I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes.
Two of my axes are #4 and #5.
When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)"
I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related.
Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable?
Cheers, Alexis
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Thanks both, makes sense! On Mon, Nov 20, 2023 at 12:17 PM Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Yes, it will only be in the daily build, not the release candidate.
—Eric
On Nov 20, 2023, at 12:05 PM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
In general, when we are in the candidate release stage, unless the developer says it is in both the upcoming release and daily, it is only in the daily. Once the release branch exists, one would have to specifically copy the development changes to the release branch as well, and we try to limit feature changes on the latter while it's in the shakeout period.
Eric will have to weigh on this one specifically, however.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2023, at 11:56 AM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Excellent, thanks!
By the way, for this and other changes made before the actual 1.7 release, will these features end up in 1.7?
On Mon, Nov 20, 2023 at 11:04 AM Eric Pettersen <pett@cgl.ucsf.edu> wrote: Hi Alexis, I added an “axisType” keyword to “measure rotation” that accepts either ‘markers’ or ‘object’ as its value. So if you use the latter value you can create an axis object directly. The default is still “markers” for backwards compatibility. This change will be in the next daily build.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 17, 2023, at 12:56 PM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Thanks Tom, that's great.
We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
I can see why you'd be ambivalent about this. The fact that it's easy to define an axis from the pair of atoms that is currently output means there's a really quick workaround anyway.
Cheers, Alexis
On Fri, Nov 17, 2023 at 11:35 AM Tom Goddard <goddard@sonic.net> wrote: Hi Alexis,
I made the "angle" command handle the measure rotation axes, so if you have two axes #3 and #4 you can just use
angle #3,4
As Elaine mentioned each axis is just a pair of atoms and now the angle command can take 4 atoms defining two vectors. We are also talking about adding an option to the measure rotation command to produce an Axis model but haven't settled on that yet (mostly because we think no one will know when to use it).
Tom
On Nov 16, 2023, at 5:35 PM, Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Alexis,
Unfortunately the measure rotation code was written long before define axes and was never updated to make them compatible. Since measure rotation has been around forever we probably are not going to change the model it makes since that will break the way people have been using it. But we ought to add an option to allow creating an axis model.
Tom
On Nov 16, 2023, at 5:26 PM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello Alexis, The axis representations from "measure rotation" are actually marker models, just two markers (dummy atoms) with a link (bond) between them, and not axis objects proper. I agree it is very confusing because they represent axes and look almost the same as the axis objects, which are cylindrical.
< https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
As I understand it, only the "define" command and the Axes/Planes/Centroids tool create axis objects proper.
That's not to disregard your suggestion, which makes sense.
However, the current workaround is to select the two markers at the ends of the "measure rotation" marker model and use "define" or the Axes/Planes/Centroids tool to create an axis object from them.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
> On Nov 16, 2023, at 5:19 PM, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote: > > Hello again, > > I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes. > > Two of my axes are #4 and #5. > > When I try to measure the angle with "angle #4 #5", I get the error: > "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)" > > I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related. > > Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable? > > Cheers, > Alexis
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participants (4)
-
Alexis Rohou -
Elaine Meng -
Eric Pettersen -
Tom Goddard