Push and pulling model/map towards/away
Hi Team, Chimera used to have a really nice feature that allowed for a model to be pushed away or pulled towards the user. How do I access this feature in ChimeraX? 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
Hi Pranav, I guess you mean "Z-translation" ... it is a little awkward but done in ChimeraX by adding Ctrl to whatever button(s) you have assigned to XY-translation. See the description of the "translate" function in the help: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> ...and perhaps also this recent post on the mailing list <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 5, 2024, at 10:11 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team, Chimera used to have a really nice feature that allowed for a model to be pushed away or pulled towards the user. How do I access this feature in ChimeraX? Best, Pranav
For moving specific models only, it's analogous: you can add Ctrl to the assignment for "translate selected models" "move picked model" etc. to switch to Z-translation. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functions> Elaine
On Jun 5, 2024, at 11:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean "Z-translation" ... it is a little awkward but done in ChimeraX by adding Ctrl to whatever button(s) you have assigned to XY-translation.
See the description of the "translate" function in the help: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
...and perhaps also this recent post on the mailing list <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 5, 2024, at 10:11 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team, Chimera used to have a really nice feature that allowed for a model to be pushed away or pulled towards the user. How do I access this feature in ChimeraX? Best, Pranav
Hi Elaine, Thanks for that information, I tried setting the middle mouse button to this mode using this command mousemode control alt middle "translate selected model" however, there is no movement in the model, instead, the i can see the clipping planes moving the side view along the Z-axis. I am using ChimeraX version 1.7.1 (2024-01-23). Have things changed since or should I be using a daily build to use this functionality? 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 Wed, Jun 5, 2024 at 7:36 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
For moving specific models only, it's analogous: you can add Ctrl to the assignment for "translate selected models" "move picked model" etc. to switch to Z-translation.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functions>
Elaine
On Jun 5, 2024, at 11:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean "Z-translation" ... it is a little awkward but done in ChimeraX by adding Ctrl to whatever button(s) you have assigned to XY-translation.
See the description of the "translate" function in the help: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
...and perhaps also this recent post on the mailing list <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 5, 2024, at 10:11 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team, Chimera used to have a really nice feature that allowed for a model to be pushed away or pulled towards the user. How do I access this feature in ChimeraX? Best, Pranav
Hi Pranav, As explained in the help and discussion links in my previous message, (1) you specifically have to press Ctrl last after all the other keys in the assignment, i.e. try translating XY and then *without* releasing those keys, add Ctrl (2) you have to drag vertically. Elaine
On Jun 5, 2024, at 1:17 PM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Thanks for that information, I tried setting the middle mouse button to this mode using this command mousemode control alt middle "translate selected model" however, there is no movement in the model, instead, the i can see the clipping planes moving the side view along the Z-axis. I am using ChimeraX version 1.7.1 (2024-01-23). Have things changed since or should I be using a daily build to use this functionality? 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 Wed, Jun 5, 2024 at 7:36 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
For moving specific models only, it's analogous: you can add Ctrl to the assignment for "translate selected models" "move picked model" etc. to switch to Z-translation.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functions>
Elaine
On Jun 5, 2024, at 11:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean "Z-translation" ... it is a little awkward but done in ChimeraX by adding Ctrl to whatever button(s) you have assigned to XY-translation.
See the description of the "translate" function in the help: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
...and perhaps also this recent post on the mailing list <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 5, 2024, at 10:11 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team, Chimera used to have a really nice feature that allowed for a model to be pushed away or pulled towards the user. How do I access this feature in ChimeraX? Best, Pranav
_______________________________________________ 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 Elaine, I did try what you suggested. I have also now installed version 1.8rc202406042103 (2024-06-04), but the same behaviour persists :( 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 Wed, Jun 5, 2024 at 9:36 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, As explained in the help and discussion links in my previous message,
(1) you specifically have to press Ctrl last after all the other keys in the assignment, i.e. try translating XY and then *without* releasing those keys, add Ctrl
(2) you have to drag vertically.
Elaine
On Jun 5, 2024, at 1:17 PM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Thanks for that information, I tried setting the middle mouse button to this mode using this command mousemode control alt middle "translate selected model" however, there is no movement in the model, instead, the i can see the clipping planes moving the side view along the Z-axis. I am using ChimeraX version 1.7.1 (2024-01-23). Have things changed since or should I be using a daily build to use this functionality? 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 Wed, Jun 5, 2024 at 7:36 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
For moving specific models only, it's analogous: you can add Ctrl to the assignment for "translate selected models" "move picked model" etc. to switch to Z-translation.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functions>
Elaine
On Jun 5, 2024, at 11:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean "Z-translation" ... it is a little awkward but done in ChimeraX by adding Ctrl to whatever button(s) you have assigned to XY-translation.
See the description of the "translate" function in the help: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
...and perhaps also this recent post on the mailing list <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 5, 2024, at 10:11 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team, Chimera used to have a really nice feature that allowed for a model to be pushed away or pulled towards the user. How do I access this feature in ChimeraX? Best, Pranav
_______________________________________________ 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/
Here;s a gif to illustrate my point 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 Wed, Jun 5, 2024 at 9:40 PM Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Elaine, I did try what you suggested. I have also now installed version 1.8rc202406042103 (2024-06-04), but the same behaviour persists :( 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 Wed, Jun 5, 2024 at 9:36 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, As explained in the help and discussion links in my previous message,
(1) you specifically have to press Ctrl last after all the other keys in the assignment, i.e. try translating XY and then *without* releasing those keys, add Ctrl
(2) you have to drag vertically.
Elaine
On Jun 5, 2024, at 1:17 PM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Thanks for that information, I tried setting the middle mouse button to this mode using this command mousemode control alt middle "translate selected model" however, there is no movement in the model, instead, the i can see the clipping planes moving the side view along the Z-axis. I am using ChimeraX version 1.7.1 (2024-01-23). Have things changed since or should I be using a daily build to use this functionality? 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 Wed, Jun 5, 2024 at 7:36 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
For moving specific models only, it's analogous: you can add Ctrl to the assignment for "translate selected models" "move picked model" etc. to switch to Z-translation.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functions>
Elaine
On Jun 5, 2024, at 11:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean "Z-translation" ... it is a little awkward but done in ChimeraX by adding Ctrl to whatever button(s) you have assigned to XY-translation.
See the description of the "translate" function in the help: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
...and perhaps also this recent post on the mailing list <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 5, 2024, at 10:11 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team, Chimera used to have a really nice feature that allowed for a model to be pushed away or pulled towards the user. How do I access this feature in ChimeraX? Best, Pranav
_______________________________________________ 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/
What is your "translate selected models" assigned to? Don't include Ctrl in that assignment. You add the Ctrl to what is assigned. Other than that I don't have advice, it works for me. E.g. I assign "translate selected models" to right mouse, and then right mouse click-drag XY translates, and right mouse (pressed first) + Ctrl (pressed last) Z-translates my selected model(s). I agree it is awkward to use, but it definitely works for me: I can see the model going front to back in the Side View. Z-translation was added before the 1.7 release, Sep 9 2023 <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> Elaine
On Jun 5, 2024, at 1:40 PM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, I did try what you suggested. I have also now installed version 1.8rc202406042103 (2024-06-04), but the same behaviour persists :( 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 Wed, Jun 5, 2024 at 9:36 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, As explained in the help and discussion links in my previous message,
(1) you specifically have to press Ctrl last after all the other keys in the assignment, i.e. try translating XY and then *without* releasing those keys, add Ctrl
(2) you have to drag vertically.
Elaine
On Jun 5, 2024, at 1:17 PM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Thanks for that information, I tried setting the middle mouse button to this mode using this command mousemode control alt middle "translate selected model" however, there is no movement in the model, instead, the i can see the clipping planes moving the side view along the Z-axis. I am using ChimeraX version 1.7.1 (2024-01-23). Have things changed since or should I be using a daily build to use this functionality? 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 Wed, Jun 5, 2024 at 7:36 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
For moving specific models only, it's analogous: you can add Ctrl to the assignment for "translate selected models" "move picked model" etc. to switch to Z-translation.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functions>
Elaine
On Jun 5, 2024, at 11:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean "Z-translation" ... it is a little awkward but done in ChimeraX by adding Ctrl to whatever button(s) you have assigned to XY-translation.
See the description of the "translate" function in the help: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
...and perhaps also this recent post on the mailing list <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 5, 2024, at 10:11 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team, Chimera used to have a really nice feature that allowed for a model to be pushed away or pulled towards the user. How do I access this feature in ChimeraX? Best, Pranav
_______________________________________________ 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, It is working correctly in your image as you see in the side view the model moves closer or further away. You are in orthograhpic projection mode so the model size is not changing in the main graphics because distance has no effect in orthographic projection. Tom
On Jun 5, 2024, at 1:46 PM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Here;s a gif to illustrate my point
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 Wed, Jun 5, 2024 at 9:40 PM Pranav Shah <p.shah.lab@gmail.com> wrote:
Hi Elaine, I did try what you suggested. I have also now installed version 1.8rc202406042103 (2024-06-04), but the same behaviour persists :( 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 Wed, Jun 5, 2024 at 9:36 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, As explained in the help and discussion links in my previous message,
(1) you specifically have to press Ctrl last after all the other keys in the assignment, i.e. try translating XY and then *without* releasing those keys, add Ctrl
(2) you have to drag vertically.
Elaine
On Jun 5, 2024, at 1:17 PM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Thanks for that information, I tried setting the middle mouse button to this mode using this command mousemode control alt middle "translate selected model" however, there is no movement in the model, instead, the i can see the clipping planes moving the side view along the Z-axis. I am using ChimeraX version 1.7.1 (2024-01-23). Have things changed since or should I be using a daily build to use this functionality? 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 Wed, Jun 5, 2024 at 7:36 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
For moving specific models only, it's analogous: you can add Ctrl to the assignment for "translate selected models" "move picked model" etc. to switch to Z-translation.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functions>
Elaine
On Jun 5, 2024, at 11:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Pranav, I guess you mean "Z-translation" ... it is a little awkward but done in ChimeraX by adding Ctrl to whatever button(s) you have assigned to XY-translation.
See the description of the "translate" function in the help: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
...and perhaps also this recent post on the mailing list <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
> On Jun 5, 2024, at 10:11 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hi Team, > Chimera used to have a really nice feature that allowed for a model to > be pushed away or pulled towards the user. How do I access this > feature in ChimeraX? > Best, > Pranav
_______________________________________________ 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/
<z-translate.gif>
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/
participants (3)
-
Elaine Meng -
Pranav Shah -
Tom Goddard