Can we navigate the protein model like in coot? spacebar jumps from residue i to residue i+1 shift-spacebar jumps from residue i to residue i-1 ctrl-g shows a tiny window where I can input 'a1' and the cofr goes to chain a residue 1 Can you point me in the right direction? Do I have to use aliases or is it something more complicated? Thanks
I don't think there is anything like that built in. It would be something like commands view :1 view :2 (etc.) ... and you can assign commands to function keys, <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functionkey> ... but I don't know how you would implement a next/previous type of thing without having to use python. Maybe others can advise. 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 Jul 2, 2025, at 10:21 AM, Murpholino Peligro via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Can we navigate the protein model like in coot?
spacebar jumps from residue i to residue i+1 shift-spacebar jumps from residue i to residue i-1 ctrl-g shows a tiny window where I can input 'a1' and the cofr goes to chain a residue 1
Can you point me in the right direction? Do I have to use aliases or is it something more complicated?
Thanks
Oh that is neat Elaine!! Not sure how exactly to do the coot-like navigation - would get complicated - but straight away I am assigning F1 and F2 to previous model (prevmodel) and next model (nextmodel), to allow switching models without using the GUI/Model Panel... these function keys add a lot of flexibility! Cheers Oli
On Jul 2, 2025, at 2:03 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I don't think there is anything like that built in. It would be something like commands
view :1 view :2 (etc.)
... and you can assign commands to function keys, <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#functionkey>
... but I don't know how you would implement a next/previous type of thing without having to use python. Maybe others can advise.
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 Jul 2, 2025, at 10:21 AM, Murpholino Peligro via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Can we navigate the protein model like in coot?
spacebar jumps from residue i to residue i+1 shift-spacebar jumps from residue i to residue i-1 ctrl-g shows a tiny window where I can input 'a1' and the cofr goes to chain a residue 1
Can you point me in the right direction? Do I have to use aliases or is it something more complicated?
Thanks
_______________________________________________ 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/
With ISOLDE, you have buttons in the toolbar that do exactly this. The corresponding commands are “isolde step next”, “isolde step prev”, and “isolde step atom-spec” to set the origin of the residue stepper to a specific residue (if you don’t use it, “next” starts at the first residue of the first chain). There are aliases to make the commands shorter (you have to declare the aliases once per session). I find that entering the next command and repeatedly pressing enter is functionally equivalent to hitting spacebar in Coot. I hope this helps, Guillaume Typed on a phone On 2 Jul 2025, at 19:23, Murpholino Peligro via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Can we navigate the protein model like in coot? spacebar jumps from residue i to residue i+1 shift-spacebar jumps from residue i to residue i-1 ctrl-g shows a tiny window where I can input 'a1' and the cofr goes to chain a residue 1 Can you point me in the right direction? Do I have to use aliases or is it something more complicated? Thanks VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ 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/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
hummmm I see there's no isolde for chimera 1.10. Can I have both versions (1.9 and 1.10) installed on linux? or should i go back to 1.9 to try this? El mié, 2 jul 2025 a la(s) 12:22 p.m., Guillaume Gaullier ( guillaume.gaullier@kemi.uu.se) escribió:
With ISOLDE, you have buttons in the toolbar that do exactly this. The corresponding commands are “isolde step next”, “isolde step prev”, and “isolde step atom-spec” to set the origin of the residue stepper to a specific residue (if you don’t use it, “next” starts at the first residue of the first chain). There are aliases to make the commands shorter (you have to declare the aliases once per session). I find that entering the next command and repeatedly pressing enter is functionally equivalent to hitting spacebar in Coot.
I hope this helps, Guillaume
Typed on a phone
On 2 Jul 2025, at 19:23, Murpholino Peligro via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Can we navigate the protein model like in coot?
spacebar jumps from residue i to residue i+1 shift-spacebar jumps from residue i to residue i-1 ctrl-g shows a tiny window where I can input 'a1' and the cofr goes to chain a residue 1
Can you point me in the right direction? Do I have to use aliases or is it something more complicated?
Thanks
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
_______________________________________________ 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/
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
Yes, you'll need to stick with 1.9 until there is a newer version of ISOLDE. That's true for all platforms, not just LInux. -- Greg On 7/2/2025 11:26 AM, Murpholino Peligro via ChimeraX-users wrote:
hummmm I see there's no isolde for chimera 1.10. Can I have both versions (1.9 and 1.10) installed on linux? or should i go back to 1.9 to try this?
El mié, 2 jul 2025 a la(s) 12:22 p.m., Guillaume Gaullier (guillaume.gaullier@kemi.uu.se) escribió:
With ISOLDE, you have buttons in the toolbar that do exactly this. The corresponding commands are “isolde step next”, “isolde step prev”, and “isolde step atom-spec” to set the origin of the residue stepper to a specific residue (if you don’t use it, “next” starts at the first residue of the first chain). There are aliases to make the commands shorter (you have to declare the aliases once per session). I find that entering the next command and repeatedly pressing enter is functionally equivalent to hitting spacebar in Coot.
I hope this helps, Guillaume
Typed on a phone
On 2 Jul 2025, at 19:23, Murpholino Peligro via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Can we navigate the protein model like in coot?
spacebar jumps from residue i to residue i+1 shift-spacebar jumps from residue i to residue i-1 ctrl-g shows a tiny window where I can input 'a1' and the cofr goes to chain a residue 1
Can you point me in the right direction? Do I have to use aliases or is it something more complicated?
Thanks
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
_______________________________________________ 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/
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
_______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
And... The Linux packages only support two kinds to be installed at the same time. The daily build and production/candidate release. If you want to have more version, you'll need to use a container. So a docker or apptainer/singularity container. The tricky part with containers is making sure you have the appropriate graphics driver installed. -- Greg On 7/2/2025 5:27 PM, Greg Couch via ChimeraX-users wrote:
Yes, you'll need to stick with 1.9 until there is a newer version of ISOLDE. That's true for all platforms, not just LInux.
-- Greg
On 7/2/2025 11:26 AM, Murpholino Peligro via ChimeraX-users wrote:
hummmm I see there's no isolde for chimera 1.10. Can I have both versions (1.9 and 1.10) installed on linux? or should i go back to 1.9 to try this?
El mié, 2 jul 2025 a la(s) 12:22 p.m., Guillaume Gaullier (guillaume.gaullier@kemi.uu.se) escribió:
With ISOLDE, you have buttons in the toolbar that do exactly this. The corresponding commands are “isolde step next”, “isolde step prev”, and “isolde step atom-spec” to set the origin of the residue stepper to a specific residue (if you don’t use it, “next” starts at the first residue of the first chain). There are aliases to make the commands shorter (you have to declare the aliases once per session). I find that entering the next command and repeatedly pressing enter is functionally equivalent to hitting spacebar in Coot.
I hope this helps, Guillaume
Typed on a phone
On 2 Jul 2025, at 19:23, Murpholino Peligro via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Can we navigate the protein model like in coot?
spacebar jumps from residue i to residue i+1 shift-spacebar jumps from residue i to residue i-1 ctrl-g shows a tiny window where I can input 'a1' and the cofr goes to chain a residue 1
Can you point me in the right direction? Do I have to use aliases or is it something more complicated?
Thanks
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
_______________________________________________ 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/
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
_______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-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 tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (5)
-
Elaine Meng -
Greg Couch -
Guillaume Gaullier -
Murpholino Peligro -
Oliver Clarke