how to hide all for a specified spec
Hi users, Often when I open a PDB, some residues are shown in both cartoon and atomic display. Often I want to hide both displays, and I can’t figure out how to do this. For instance open 7ubj hide #1 // hides only the atoms hide #1 all // gives an error hide #1 cartoons // this seems to be the only way to hide the cartoons? same story with, for instance hide #1/A Am I missing something? I’m running 1.11.1 on Mac. Thanks, Daniel
Hi Daniel, Default for "hide" is hiding atoms, but you can specify cartoons, atoms, or both (as well as surfaces etc.). See documentation for "hide" by using command "help hide" or viewing the copy on our website: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html> Examples: hide #1 target ac -- same as -- hide #1 atoms,cartoons If you want to include more than one type of display, target is the shorter way. For all kinds of display types, hide #1 target abpcs Now, you could hide the entire model and all of its displays with hide #1 models ...same as un-checking the "eye" column in the Models panel ... but then you would need to re-enable model display to show any of its underlying display types: atoms, cartoons, etc. (it's a display hierarchy). 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 Apr 21, 2026, at 12:30 PM, Daniel David Richman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi users,
Often when I open a PDB, some residues are shown in both cartoon and atomic display. Often I want to hide both displays, and I can’t figure out how to do this. For instance
open 7ubj hide #1 // hides only the atoms hide #1 all // gives an error hide #1 cartoons // this seems to be the only way to hide the cartoons?
same story with, for instance hide #1/A
Am I missing something? I’m running 1.11.1 on Mac.
Thanks, Daniel\
And what is the difference between 'hide #1 models' and 'hide #!1 models' (with an exclamation mark, reported in the Log when toggling the Eye checkbox of an entire model in the Models panel)? I looked for it in the documentation, but it’s not explained (at least not in the atom-spec page, maybe it’s elsewhere). Thanks! Guillaume
On 21 Apr 2026, at 22:06, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Daniel, Default for "hide" is hiding atoms, but you can specify cartoons, atoms, or both (as well as surfaces etc.). See documentation for "hide" by using command "help hide" or viewing the copy on our website: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html>
Examples:
hide #1 target ac
-- same as --
hide #1 atoms,cartoons
If you want to include more than one type of display, target is the shorter way. For all kinds of display types,
hide #1 target abpcs
Now, you could hide the entire model and all of its displays with
hide #1 models
...same as un-checking the "eye" column in the Models panel ... but then you would need to re-enable model display to show any of its underlying display types: atoms, cartoons, etc. (it's a display hierarchy).
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 Apr 21, 2026, at 12:30 PM, Daniel David Richman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi users,
Often when I open a PDB, some residues are shown in both cartoon and atomic display. Often I want to hide both displays, and I can’t figure out how to do this. For instance
open 7ubj hide #1 // hides only the atoms hide #1 all // gives an error hide #1 cartoons // this seems to be the only way to hide the cartoons?
same story with, for instance hide #1/A
Am I missing something? I’m running 1.11.1 on Mac.
Thanks, Daniel\
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Hi Guillaume, 'hide #1 models' will set the display flag to false for #1 *and all its sub-models*. 'hide #!1 models' will only set it for the top-level model #1. In most cases it makes no difference, but it can do when you have a more complex scene... for a trivial example, say you have a structure where you've hidden the sub-model containing the missing-structure pseudobonds. Then "hide #1 models; show #1 models" won't be perfectly reversible (the pseudobond model will be displayed by the second command), where "hide #!1 models; show #!1 models" will be. Best, Tristan On Wed, Apr 22, 2026 at 5:58 AM Guillaume Gaullier via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
And what is the difference between 'hide #1 models' and 'hide #!1 models' (with an exclamation mark, reported in the Log when toggling the Eye checkbox of an entire model in the Models panel)?
I looked for it in the documentation, but it’s not explained (at least not in the atom-spec page, maybe it’s elsewhere).
Thanks!
Guillaume
On 21 Apr 2026, at 22:06, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Daniel, Default for "hide" is hiding atoms, but you can specify cartoons, atoms, or both (as well as surfaces etc.). See documentation for "hide" by using command "help hide" or viewing the copy on our website: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html>
Examples:
hide #1 target ac
-- same as --
hide #1 atoms,cartoons
If you want to include more than one type of display, target is the shorter way. For all kinds of display types,
hide #1 target abpcs
Now, you could hide the entire model and all of its displays with
hide #1 models
...same as un-checking the "eye" column in the Models panel ... but then you would need to re-enable model display to show any of its underlying display types: atoms, cartoons, etc. (it's a display hierarchy).
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 Apr 21, 2026, at 12:30 PM, Daniel David Richman via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi users,
Often when I open a PDB, some residues are shown in both cartoon and atomic display. Often I want to hide both displays, and I can’t figure out how to do this. For instance
open 7ubj hide #1 // hides only the atoms hide #1 all // gives an error hide #1 cartoons // this seems to be the only way to hide the cartoons?
same story with, for instance hide #1/A
Am I missing something? I’m running 1.11.1 on Mac.
Thanks, Daniel\
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The description of #! is in the second paragraph under the Hierarchical Specifiers table, although it's easy to miss: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy> 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 Apr 22, 2026, at 3:23 AM, Tristan Croll <tcroll@altoslabs.com> wrote:
Hi Guillaume, 'hide #1 models' will set the display flag to false for #1 *and all its sub-models*. 'hide #!1 models' will only set it for the top-level model #1. In most cases it makes no difference, but it can do when you have a more complex scene... for a trivial example, say you have a structure where you've hidden the sub-model containing the missing-structure pseudobonds. Then "hide #1 models; show #1 models" won't be perfectly reversible (the pseudobond model will be displayed by the second command), where "hide #!1 models; show #!1 models" will be. Best, Tristan
On Wed, Apr 22, 2026 at 5:58 AM Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: And what is the difference between 'hide #1 models' and 'hide #!1 models' (with an exclamation mark, reported in the Log when toggling the Eye checkbox of an entire model in the Models panel)?
I looked for it in the documentation, but it’s not explained (at least not in the atom-spec page, maybe it’s elsewhere).
Thanks!
Guillaume
On 21 Apr 2026, at 22:06, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Daniel, Default for "hide" is hiding atoms, but you can specify cartoons, atoms, or both (as well as surfaces etc.). See documentation for "hide" by using command "help hide" or viewing the copy on our website: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/show.html>
Examples:
hide #1 target ac
-- same as --
hide #1 atoms,cartoons
If you want to include more than one type of display, target is the shorter way. For all kinds of display types,
hide #1 target abpcs
Now, you could hide the entire model and all of its displays with
hide #1 models
...same as un-checking the "eye" column in the Models panel ... but then you would need to re-enable model display to show any of its underlying display types: atoms, cartoons, etc. (it's a display hierarchy).
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 Apr 21, 2026, at 12:30 PM, Daniel David Richman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi users,
Often when I open a PDB, some residues are shown in both cartoon and atomic display. Often I want to hide both displays, and I can’t figure out how to do this. For instance
open 7ubj hide #1 // hides only the atoms hide #1 all // gives an error hide #1 cartoons // this seems to be the only way to hide the cartoons?
same story with, for instance hide #1/A
Am I missing something? I’m running 1.11.1 on Mac.
Thanks, Daniel\
_______________________________________________ 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/
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.
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 to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
participants (4)
-
Daniel David Richman -
Elaine Meng -
Guillaume Gaullier -
Tristan Croll