Rotation using left mouse button
Hello, In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn't suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance. With kind regards, Yorick van Hazendonk
Hi Yorick, That is an annoying problem. I fixed a bug in ChimeraX that caused the rotation axis to change when a part of your structure passes in front and 3d labels are being shown. That fix is in the ChimeraX daily build. In your case are there 3d labels shown? If so get the ChimeraX daily build to fix the problem. The default rotation center mode in ChimeraX is called "front center" -- it tries to rotate about the frontmost atoms/ribbon/surface visible in the center of of your graphics window. But it only is supposed to check which objects are in the center when you translate the the scene. If you do a mouse rotation, then another rotation, then another, it should keep the rotation center the same. There are other rotation center modes you may prefer. See the ChimeraX cofr (center of rotation) command. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cofr.html For example there is a Pivot mouse mode in the "Right mouse" toolbar that sets a fixed center of rotation point on the atom you click using the right mouse button (or Command-click on Mac). Tom
On Feb 25, 2025, at 3:25 AM, y.v.hazendonk--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn’t suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance.
With kind regards, Yorick van Hazendonk _______________________________________________ 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/
Hi Tom, I can confirm this behaviour even in the case of isosurface renders of say MRC files when the contour is lowered, the COFR automatically locks on to center that is not the center of the object e.g. noise artefacts. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK On Tue, Feb 25, 2025 at 7:55 PM Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Yorick,
That is an annoying problem. I fixed a bug in ChimeraX that caused the rotation axis to change when a part of your structure passes in front and 3d labels are being shown. That fix is in the ChimeraX daily build. In your case are there 3d labels shown? If so get the ChimeraX daily build to fix the problem.
The default rotation center mode in ChimeraX is called "front center" -- it tries to rotate about the frontmost atoms/ribbon/surface visible in the center of of your graphics window. But it only is supposed to check which objects are in the center when you translate the the scene. If you do a mouse rotation, then another rotation, then another, it should keep the rotation center the same. There are other rotation center modes you may prefer. See the ChimeraX cofr (center of rotation) command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cofr.html
For example there is a Pivot mouse mode in the "Right mouse" toolbar that sets a fixed center of rotation point on the atom you click using the right mouse button (or Command-click on Mac).
Tom
On Feb 25, 2025, at 3:25 AM, y.v.hazendonk--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn’t suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance.
With kind regards, Yorick van Hazendonk _______________________________________________ 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/
_______________________________________________ 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 Pranav, The center of rotation calculation knows nothing about "noise". If there is a speck of a volume contour surface in the center of the view when the center of rotation is computed then it will use that speck as the center of rotation. Tom
On Feb 26, 2025, at 2:45 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, I can confirm this behaviour even in the case of isosurface renders of say MRC files when the contour is lowered, the COFR automatically locks on to center that is not the center of the object e.g. noise artefacts. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Tue, Feb 25, 2025 at 7:55 PM Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Yorick,
That is an annoying problem. I fixed a bug in ChimeraX that caused the rotation axis to change when a part of your structure passes in front and 3d labels are being shown. That fix is in the ChimeraX daily build. In your case are there 3d labels shown? If so get the ChimeraX daily build to fix the problem.
The default rotation center mode in ChimeraX is called "front center" -- it tries to rotate about the frontmost atoms/ribbon/surface visible in the center of of your graphics window. But it only is supposed to check which objects are in the center when you translate the the scene. If you do a mouse rotation, then another rotation, then another, it should keep the rotation center the same. There are other rotation center modes you may prefer. See the ChimeraX cofr (center of rotation) command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cofr.html
For example there is a Pivot mouse mode in the "Right mouse" toolbar that sets a fixed center of rotation point on the atom you click using the right mouse button (or Command-click on Mac).
Tom
On Feb 25, 2025, at 3:25 AM, y.v.hazendonk--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn’t suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance.
With kind regards, Yorick van Hazendonk _______________________________________________ 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/
_______________________________________________ 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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... and therefore changing your "cofr" method to centerOfView (rather than the default frontCenter) could possibly work better for you. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Feb 26, 2025, at 11:39 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav,
The center of rotation calculation knows nothing about "noise". If there is a speck of a volume contour surface in the center of the view when the center of rotation is computed then it will use that speck as the center of rotation.
Tom
On Feb 26, 2025, at 2:45 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, I can confirm this behaviour even in the case of isosurface renders of say MRC files when the contour is lowered, the COFR automatically locks on to center that is not the center of the object e.g. noise artefacts. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Tue, Feb 25, 2025 at 7:55 PM Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Yorick,
That is an annoying problem. I fixed a bug in ChimeraX that caused the rotation axis to change when a part of your structure passes in front and 3d labels are being shown. That fix is in the ChimeraX daily build. In your case are there 3d labels shown? If so get the ChimeraX daily build to fix the problem.
The default rotation center mode in ChimeraX is called "front center" -- it tries to rotate about the frontmost atoms/ribbon/surface visible in the center of of your graphics window. But it only is supposed to check which objects are in the center when you translate the the scene. If you do a mouse rotation, then another rotation, then another, it should keep the rotation center the same. There are other rotation center modes you may prefer. See the ChimeraX cofr (center of rotation) command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cofr.html
For example there is a Pivot mouse mode in the "Right mouse" toolbar that sets a fixed center of rotation point on the atom you click using the right mouse button (or Command-click on Mac).
Tom
On Feb 25, 2025, at 3:25 AM, y.v.hazendonk--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn’t suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance.
With kind regards, Yorick van Hazendonk _______________________________________________ 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/
_______________________________________________ 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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_______________________________________________ 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 Eric, While center of view is an option, you just exchange one sometimes wrong depth for the center of rotation for a more frequently wrong depth. Here's how the ChimeraX cofr command documentation describes the center of view setting centerOfView – keep updating the center of rotation to the middle of the graphics window in X and Y (screen coordinates), with Z (depth) halfway between the near and far clipping planes. If only one of the near/far planes is active, the center of rotation depth tracks that of the active plane. If neither clipping plane is active, the center of rotation depth remains constant starting from the center of the bounding box of the first model opened, or if the method was switched, from the previous center of rotation. https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cofr.html The basic trouble with all automatic center of rotation calculations is the software does not know what your eyes are focusing on. Are you looking past a ribbon in front into a binding site behind? If you like maximum control you might want to always explicitly choose the center of rotation by clicking on an atom or ribbon or surface point using the "Pivot" mouse mode in the Right Mouse toolbar. Then a right click on an object sets the center of rotation point. Tedious but the behavior is easily predictable, no magic choosing of the rotation center. My best suggestion is that if you understand how the default "front center" rotation works (e.g. when it updates the center and how it calculates it) then you will rarely get the wrong center. But the behavior not obvious and studying the "cofr" documentation may be needed to understand it. Tom
On Feb 26, 2025, at 11:43 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
... and therefore changing your "cofr" method to centerOfView (rather than the default frontCenter) could possibly work better for you.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 26, 2025, at 11:39 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav,
The center of rotation calculation knows nothing about "noise". If there is a speck of a volume contour surface in the center of the view when the center of rotation is computed then it will use that speck as the center of rotation.
Tom
On Feb 26, 2025, at 2:45 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, I can confirm this behaviour even in the case of isosurface renders of say MRC files when the contour is lowered, the COFR automatically locks on to center that is not the center of the object e.g. noise artefacts. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Tue, Feb 25, 2025 at 7:55 PM Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Yorick,
That is an annoying problem. I fixed a bug in ChimeraX that caused the rotation axis to change when a part of your structure passes in front and 3d labels are being shown. That fix is in the ChimeraX daily build. In your case are there 3d labels shown? If so get the ChimeraX daily build to fix the problem.
The default rotation center mode in ChimeraX is called "front center" -- it tries to rotate about the frontmost atoms/ribbon/surface visible in the center of of your graphics window. But it only is supposed to check which objects are in the center when you translate the the scene. If you do a mouse rotation, then another rotation, then another, it should keep the rotation center the same. There are other rotation center modes you may prefer. See the ChimeraX cofr (center of rotation) command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cofr.html
For example there is a Pivot mouse mode in the "Right mouse" toolbar that sets a fixed center of rotation point on the atom you click using the right mouse button (or Command-click on Mac).
Tom
On Feb 25, 2025, at 3:25 AM, y.v.hazendonk--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn’t suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance.
With kind regards, Yorick van Hazendonk _______________________________________________ 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/
_______________________________________________ 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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YMMV... for my money, I find "centerofview" much more intuitive and amenable to precise navigation within a structure, and have it set as the default, but this will of course depend on personal preference (e.g. I use Coot a lot for building, so I am used to having the center of rotation more or less locked to the center of view). It is also useful to have "showpivot" bound to an alias or button, so that you can easily switch on or off marking the center of rotation while navigating. Cheers Oli
On Feb 26, 2025, at 3:05 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Eric,
While center of view is an option, you just exchange one sometimes wrong depth for the center of rotation for a more frequently wrong depth. Here's how the ChimeraX cofr command documentation describes the center of view setting
centerOfView – keep updating the center of rotation to the middle of the graphics window in X and Y (screen coordinates), with Z (depth) halfway between the near and far clipping planes. If only one of the near/far planes is active, the center of rotation depth tracks that of the active plane. If neither clipping plane is active, the center of rotation depth remains constant starting from the center of the bounding box of the first model opened, or if the method was switched, from the previous center of rotation.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cofr.html
The basic trouble with all automatic center of rotation calculations is the software does not know what your eyes are focusing on. Are you looking past a ribbon in front into a binding site behind? If you like maximum control you might want to always explicitly choose the center of rotation by clicking on an atom or ribbon or surface point using the "Pivot" mouse mode in the Right Mouse toolbar. Then a right click on an object sets the center of rotation point. Tedious but the behavior is easily predictable, no magic choosing of the rotation center.
My best suggestion is that if you understand how the default "front center" rotation works (e.g. when it updates the center and how it calculates it) then you will rarely get the wrong center. But the behavior not obvious and studying the "cofr" documentation may be needed to understand it.
Tom
On Feb 26, 2025, at 11:43 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
... and therefore changing your "cofr" method to centerOfView (rather than the default frontCenter) could possibly work better for you.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Feb 26, 2025, at 11:39 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav,
The center of rotation calculation knows nothing about "noise". If there is a speck of a volume contour surface in the center of the view when the center of rotation is computed then it will use that speck as the center of rotation.
Tom
On Feb 26, 2025, at 2:45 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tom, I can confirm this behaviour even in the case of isosurface renders of say MRC files when the contour is lowered, the COFR automatically locks on to center that is not the center of the object e.g. noise artefacts. Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
On Tue, Feb 25, 2025 at 7:55 PM Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Yorick,
That is an annoying problem. I fixed a bug in ChimeraX that caused the rotation axis to change when a part of your structure passes in front and 3d labels are being shown. That fix is in the ChimeraX daily build. In your case are there 3d labels shown? If so get the ChimeraX daily build to fix the problem.
The default rotation center mode in ChimeraX is called "front center" -- it tries to rotate about the frontmost atoms/ribbon/surface visible in the center of of your graphics window. But it only is supposed to check which objects are in the center when you translate the the scene. If you do a mouse rotation, then another rotation, then another, it should keep the rotation center the same. There are other rotation center modes you may prefer. See the ChimeraX cofr (center of rotation) command.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/cofr.html
For example there is a Pivot mouse mode in the "Right mouse" toolbar that sets a fixed center of rotation point on the atom you click using the right mouse button (or Command-click on Mac).
Tom
On Feb 25, 2025, at 3:25 AM, y.v.hazendonk--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn’t suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance.
With kind regards, Yorick van Hazendonk _______________________________________________ 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/
_______________________________________________ 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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participants (5)
-
Eric Pettersen -
Oliver Clarke -
Pranav Shah -
Tom Goddard -
y.v.hazendonk＠nki.nl