focus and set pivot functions
Hello, I have used the old Chimera quite a bit and I'm trying to get used to ChimeraX. There are a couple of tools that I found very useful in the old chimera: "focus" and "set pivot". Both were under the "Actions" menu and, with large structures like the ribosome, these two tools allowed me to quickly inspect any residues that were selected with any other tools. "Focus" is not there anymore and while "set pivot" is, it doesn´t seem to work as it used to. I wonder if these tools, in their old flavors, are still available in ChimeraX. best, Antón -- Antón Vila-Sanjurjo, PhD Profesor del Area de Genética Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2267 e-mail: anton.vila@udc.es
Hi Antón, ChimeraX menu "Actions... View" is meant to be the same as Chimera's Focus, and as far as I know "Actions... Set Pivot" should also be the same: change center of rotation to a fixed point that is the center of the selected items (if there is a selection). Actions menu: <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions> There might be slight differences of how the pivot center is calculated, but I wouldn't expect it to be noticeable. Can you say more about why you think it is different? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 19, 2021, at 1:29 PM, Antón Vila-Sanjurjo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have used the old Chimera quite a bit and I'm trying to get used to ChimeraX. There are a couple of tools that I found very useful in the old chimera: "focus" and "set pivot". Both were under the "Actions" menu and, with large structures like the ribosome, these two tools allowed me to quickly inspect any residues that were selected with any other tools. "Focus" is not there anymore and while "set pivot" is, it doesn´t seem to work as it used to. I wonder if these tools, in their old flavors, are still available in ChimeraX. best, Antón
Hi Elaine, Thanks for your help! I got it to work right, I think that the problem was due to the fact that there were two symmetry-related assemblies in the structure I used and I was selecting the same chain in both assemblies. Antón On 20/12/21 17:19, Elaine Meng wrote:
Hi Antón, ChimeraX menu "Actions... View" is meant to be the same as Chimera's Focus, and as far as I know "Actions... Set Pivot" should also be the same: change center of rotation to a fixed point that is the center of the selected items (if there is a selection).
Actions menu: <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions>
There might be slight differences of how the pivot center is calculated, but I wouldn't expect it to be noticeable. Can you say more about why you think it is different?
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 19, 2021, at 1:29 PM, Antón Vila-Sanjurjo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have used the old Chimera quite a bit and I'm trying to get used to ChimeraX. There are a couple of tools that I found very useful in the old chimera: "focus" and "set pivot". Both were under the "Actions" menu and, with large structures like the ribosome, these two tools allowed me to quickly inspect any residues that were selected with any other tools. "Focus" is not there anymore and while "set pivot" is, it doesn´t seem to work as it used to. I wonder if these tools, in their old flavors, are still available in ChimeraX. best, Antón
-- Antón Vila-Sanjurjo, PhD Profesor del Area de Genética Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2267 e-mail: anton.vila@udc.es
Hi Elaine, I have noticed that the "Distances" window does not update new distances as I create them, so I have to keep closing and re-opening the window from the Tools menu. This wasn't a problem in the old Chimera. best, Antón On 21/12/21 16:44, Antón Vila-Sanjurjo wrote:
Hi Elaine,
Thanks for your help! I got it to work right, I think that the problem was due to the fact that there were two symmetry-related assemblies in the structure I used and I was selecting the same chain in both assemblies.
Antón
On 20/12/21 17:19, Elaine Meng wrote:
Hi Antón, ChimeraX menu "Actions... View" is meant to be the same as Chimera's Focus, and as far as I know "Actions... Set Pivot" should also be the same: change center of rotation to a fixed point that is the center of the selected items (if there is a selection).
Actions menu: <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions>
There might be slight differences of how the pivot center is calculated, but I wouldn't expect it to be noticeable. Can you say more about why you think it is different?
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 19, 2021, at 1:29 PM, Antón Vila-Sanjurjo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have used the old Chimera quite a bit and I'm trying to get used to ChimeraX. There are a couple of tools that I found very useful in the old chimera: "focus" and "set pivot". Both were under the "Actions" menu and, with large structures like the ribosome, these two tools allowed me to quickly inspect any residues that were selected with any other tools. "Focus" is not there anymore and while "set pivot" is, it doesn´t seem to work as it used to. I wonder if these tools, in their old flavors, are still available in ChimeraX. best, Antón
-- Antón Vila-Sanjurjo, PhD Profesor del Area de Genética Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2267 e-mail: anton.vila@udc.es
Hi Antón, For things like this that are clearly bugs, please use menu: Help... Report a Bug (instead of sending e-mail here). Although I can answer questions about using the program, I'm not a programmer so I can't address this directly. Also, it is good to put it in the bug database so that we can better track when it gets done! Bug reporting is also better because it automatically includes your program version and platform (e.g. Windows, Linux, or Mac). Please include a short description in the form, and also your e-mail address if you want feedback. I don't think it applies in this case, but when the bug depends on specific data, you can also attach a data file or session file to report. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 30, 2021, at 6:10 AM, Antón Vila-Sanjurjo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I have noticed that the "Distances" window does not update new distances as I create them, so I have to keep closing and re-opening the window from the Tools menu. This wasn't a problem in the old Chimera.
best,
Antón
absolutely! best Antón On 30/12/21 18:48, Elaine Meng wrote:
Hi Antón, For things like this that are clearly bugs, please use menu: Help... Report a Bug (instead of sending e-mail here). Although I can answer questions about using the program, I'm not a programmer so I can't address this directly. Also, it is good to put it in the bug database so that we can better track when it gets done!
Bug reporting is also better because it automatically includes your program version and platform (e.g. Windows, Linux, or Mac). Please include a short description in the form, and also your e-mail address if you want feedback.
I don't think it applies in this case, but when the bug depends on specific data, you can also attach a data file or session file to report.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 30, 2021, at 6:10 AM, Antón Vila-Sanjurjo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I have noticed that the "Distances" window does not update new distances as I create them, so I have to keep closing and re-opening the window from the Tools menu. This wasn't a problem in the old Chimera.
best,
Antón
-- Antón Vila-Sanjurjo, PhD Profesor del Area de Genética Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2267 e-mail: anton.vila@udc.es
Hi Elaine, I regularly have many ribosomal models opened at the same time, with hundreds of different chains. The "Select Chains" display does not help at all in chain selection because the chains don't fit in the screen and there is no way to scroll down to find chains in the "models" with high numbers. A similar problem occurs while selecting chains in the Matchmaker interface. The "Sequence viewer" displays chains in a much better fashion because there is an option to scroll down. Would it be possible to fix these issues? best, Antón
Hi Antón, I will make a bug report for this in a few minutes and include your e-mail address so that you will receive any notifications. In the meanwhile, for selection, try command "log chains" to show a table in the Log (which is scrollable) to show the ID for each chain in the lefthand column -- in the table you can click each ID to select that chain. If you specify multiple models it will show a table for each model. Then with the help of the chain table information, you can use the "matchmaker" command to specify the chains that you want. log chains: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#metadata> matchmaker command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 30, 2021, at 6:31 AM, Antón Vila-Sanjurjo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I regularly have many ribosomal models opened at the same time, with hundreds of different chains. The "Select Chains" display does not help at all in chain selection because the chains don't fit in the screen and there is no way to scroll down to find chains in the "models" with high numbers. A similar problem occurs while selecting chains in the Matchmaker interface. The "Sequence viewer" displays chains in a much better fashion because there is an option to scroll down. Would it be possible to fix these issues?
best,
Antón
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
thanks! Antón On 20/12/21 17:19, Elaine Meng wrote:
Hi Antón, ChimeraX menu "Actions... View" is meant to be the same as Chimera's Focus, and as far as I know "Actions... Set Pivot" should also be the same: change center of rotation to a fixed point that is the center of the selected items (if there is a selection).
Actions menu: <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions>
There might be slight differences of how the pivot center is calculated, but I wouldn't expect it to be noticeable. Can you say more about why you think it is different?
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 19, 2021, at 1:29 PM, Antón Vila-Sanjurjo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I have used the old Chimera quite a bit and I'm trying to get used to ChimeraX. There are a couple of tools that I found very useful in the old chimera: "focus" and "set pivot". Both were under the "Actions" menu and, with large structures like the ribosome, these two tools allowed me to quickly inspect any residues that were selected with any other tools. "Focus" is not there anymore and while "set pivot" is, it doesn´t seem to work as it used to. I wonder if these tools, in their old flavors, are still available in ChimeraX. best, Antón
-- Antón Vila-Sanjurjo, PhD Profesor del Area de Genética Departamento de Bioloxía Facultade de Ciencias Universidade da Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain). tlf: (34) 981-167000 ext:2267 e-mail: anton.vila@udc.es
participants (2)
-
Antón Vila-Sanjurjo -
Elaine Meng