Bond between two sequential residues
Hello, When I hide the backbone and choose to show side chain and base any sequential residues shown have a small line between the CA's. I can select them, but not delete them or hide them as an atom or bond, only hide sel, but when the selection they are a part of is hidden and reshown they reappear. I can also assign them as a selector and hide/show them, but also as soon as I hide and reshow the selection they are a part of they reappear and the designated selector for them is gone from the list. I want to retain the side chain and base appearance but lose these lines permanently. Any help would be appreciated. Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University
Hi Derek, Those are "chain trace" pseudobonds. <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> There are several ways to hide pseudobonds selectively or collectively, e.g. in the Model Panel, use the disclosure triangle to show the "chain trace" submodel of your atomic model, and uncheck the shown checkbox (the column under the eye icon). That hides the whole trace model so that they won't reappear when their atoms are hidden and re-shown. You could also hide the trace model with a command, e.g. if it is model #1.2, then hide #1.1 model If you just instead used hide #1.1 ... that would not hide it at the model level, but all the pseudobonds in that model individually. The reason for separate model level and individual display level is that toggling the model level will retain any specific on/off settings, e.g. if you had only specific ones hidden and others shown. hide @ca pseudobonds ... would hide all pseudobonds between CA atoms, leaving any others shown (h-bonds, metal coordination, etc.). You could also close it close #1.1 ...but then it could automatically regenerate if you are showing CA atoms but not the other backbone atoms between them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2020, at 3:19 PM, Derek Harris <derek.harris@aggiemail.usu.edu> wrote:
Hello,
When I hide the backbone and choose to show side chain and base any sequential residues shown have a small line between the CA's. I can select them, but not delete them or hide them as an atom or bond, only hide sel, but when the selection they are a part of is hidden and reshown they reappear. I can also assign them as a selector and hide/show them, but also as soon as I hide and reshow the selection they are a part of they reappear and the designated selector for them is gone from the list.
I want to retain the side chain and base appearance but lose these lines permanently. Any help would be appreciated.
Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you Elaine for the detailed response. While all of these options work as intended, they don't quite seem to solve my problem. In my movie I am hiding a selection and then reshowing it. While it is hidden I can't control the pseudobonds and I can't seem to hide them in a single line command without a wait 1, which shows them for that 1s. Am I missing something or is this just something I need to work around? Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University On Thu, Jul 16, 2020 at 4:42 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Derek, Those are "chain trace" pseudobonds. <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>
There are several ways to hide pseudobonds selectively or collectively, e.g. in the Model Panel, use the disclosure triangle to show the "chain trace" submodel of your atomic model, and uncheck the shown checkbox (the column under the eye icon). That hides the whole trace model so that they won't reappear when their atoms are hidden and re-shown. You could also hide the trace model with a command, e.g. if it is model #1.2, then
hide #1.1 model
If you just instead used
hide #1.1
... that would not hide it at the model level, but all the pseudobonds in that model individually. The reason for separate model level and individual display level is that toggling the model level will retain any specific on/off settings, e.g. if you had only specific ones hidden and others shown.
hide @ca pseudobonds
... would hide all pseudobonds between CA atoms, leaving any others shown (h-bonds, metal coordination, etc.).
You could also close it
close #1.1
...but then it could automatically regenerate if you are showing CA atoms but not the other backbone atoms between them.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2020, at 3:19 PM, Derek Harris < derek.harris@aggiemail.usu.edu> wrote:
Hello,
When I hide the backbone and choose to show side chain and base any sequential residues shown have a small line between the CA's. I can select them, but not delete them or hide them as an atom or bond, only hide sel, but when the selection they are a part of is hidden and reshown they reappear. I can also assign them as a selector and hide/show them, but also as soon as I hide and reshow the selection they are a part of they reappear and the designated selector for them is gone from the list.
I want to retain the side chain and base appearance but lose these lines permanently. Any help would be appreciated.
Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Derek, The way to suppress frame drawing is to combine multiple commands on the same line separated by semicolons. That prevents display of the intermediate states. Tips for ChimeraX command files: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-f...> I hope this helps, Elaine
On Jul 16, 2020, at 7:16 PM, Derek Harris <derek.harris@aggiemail.usu.edu> wrote:
Thank you Elaine for the detailed response. While all of these options work as intended, they don't quite seem to solve my problem. In my movie I am hiding a selection and then reshowing it. While it is hidden I can't control the pseudobonds and I can't seem to hide them in a single line command without a wait 1, which shows them for that 1s. Am I missing something or is this just something I need to work around?
Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University
On Thu, Jul 16, 2020 at 4:42 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Derek, Those are "chain trace" pseudobonds. <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>
There are several ways to hide pseudobonds selectively or collectively, e.g. in the Model Panel, use the disclosure triangle to show the "chain trace" submodel of your atomic model, and uncheck the shown checkbox (the column under the eye icon). That hides the whole trace model so that they won't reappear when their atoms are hidden and re-shown. You could also hide the trace model with a command, e.g. if it is model #1.2, then
hide #1.1 model
If you just instead used
hide #1.1
... that would not hide it at the model level, but all the pseudobonds in that model individually. The reason for separate model level and individual display level is that toggling the model level will retain any specific on/off settings, e.g. if you had only specific ones hidden and others shown.
hide @ca pseudobonds
... would hide all pseudobonds between CA atoms, leaving any others shown (h-bonds, metal coordination, etc.).
You could also close it
close #1.1
...but then it could automatically regenerate if you are showing CA atoms but not the other backbone atoms between them.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2020, at 3:19 PM, Derek Harris <derek.harris@aggiemail.usu.edu> wrote:
Hello,
When I hide the backbone and choose to show side chain and base any sequential residues shown have a small line between the CA's. I can select them, but not delete them or hide them as an atom or bond, only hide sel, but when the selection they are a part of is hidden and reshown they reappear. I can also assign them as a selector and hide/show them, but also as soon as I hide and reshow the selection they are a part of they reappear and the designated selector for them is gone from the list.
I want to retain the side chain and base appearance but lose these lines permanently. Any help would be appreciated.
Hi Derek, I see your problem is tricky because the chain trace pseudobonds are not created until the structure is displayed and needs them. So you can't hide them until after they appear. Here is the magic incantation to stop the chain trace pseudobonds from being created: setattr #1 model autochain false Tom
On Jul 16, 2020, at 7:16 PM, Derek Harris <derek.harris@aggiemail.usu.edu> wrote:
Thank you Elaine for the detailed response. While all of these options work as intended, they don't quite seem to solve my problem. In my movie I am hiding a selection and then reshowing it. While it is hidden I can't control the pseudobonds and I can't seem to hide them in a single line command without a wait 1, which shows them for that 1s. Am I missing something or is this just something I need to work around?
Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University
On Thu, Jul 16, 2020 at 4:42 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Derek, Those are "chain trace" pseudobonds. <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>>
There are several ways to hide pseudobonds selectively or collectively, e.g. in the Model Panel, use the disclosure triangle to show the "chain trace" submodel of your atomic model, and uncheck the shown checkbox (the column under the eye icon). That hides the whole trace model so that they won't reappear when their atoms are hidden and re-shown. You could also hide the trace model with a command, e.g. if it is model #1.2, then
hide #1.1 model
If you just instead used
hide #1.1
... that would not hide it at the model level, but all the pseudobonds in that model individually. The reason for separate model level and individual display level is that toggling the model level will retain any specific on/off settings, e.g. if you had only specific ones hidden and others shown.
hide @ca pseudobonds
... would hide all pseudobonds between CA atoms, leaving any others shown (h-bonds, metal coordination, etc.).
You could also close it
close #1.1
...but then it could automatically regenerate if you are showing CA atoms but not the other backbone atoms between them.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2020, at 3:19 PM, Derek Harris <derek.harris@aggiemail.usu.edu <mailto:derek.harris@aggiemail.usu.edu>> wrote:
Hello,
When I hide the backbone and choose to show side chain and base any sequential residues shown have a small line between the CA's. I can select them, but not delete them or hide them as an atom or bond, only hide sel, but when the selection they are a part of is hidden and reshown they reappear. I can also assign them as a selector and hide/show them, but also as soon as I hide and reshow the selection they are a part of they reappear and the designated selector for them is gone from the list.
I want to retain the side chain and base appearance but lose these lines permanently. Any help would be appreciated.
Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Tom, I had forgotten about the autochain attribute! Here's the description of the "setattr" (set attribute) command, as well as a list of selected attributes and what they mean: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html> <http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> <http://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#model> Elaine
On Jul 17, 2020, at 9:19 AM, Tom Goddard <goddard@sonic.net> wrote:
Hi Derek,
I see your problem is tricky because the chain trace pseudobonds are not created until the structure is displayed and needs them. So you can't hide them until after they appear. Here is the magic incantation to stop the chain trace pseudobonds from being created:
setattr #1 model autochain false
Tom
On Jul 16, 2020, at 7:16 PM, Derek Harris <derek.harris@aggiemail.usu.edu> wrote:
Thank you Elaine for the detailed response. While all of these options work as intended, they don't quite seem to solve my problem. In my movie I am hiding a selection and then reshowing it. While it is hidden I can't control the pseudobonds and I can't seem to hide them in a single line command without a wait 1, which shows them for that 1s. Am I missing something or is this just something I need to work around?
Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University
On Thu, Jul 16, 2020 at 4:42 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Derek, Those are "chain trace" pseudobonds. <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>
There are several ways to hide pseudobonds selectively or collectively, e.g. in the Model Panel, use the disclosure triangle to show the "chain trace" submodel of your atomic model, and uncheck the shown checkbox (the column under the eye icon). That hides the whole trace model so that they won't reappear when their atoms are hidden and re-shown. You could also hide the trace model with a command, e.g. if it is model #1.2, then
hide #1.1 model
If you just instead used
hide #1.1
... that would not hide it at the model level, but all the pseudobonds in that model individually. The reason for separate model level and individual display level is that toggling the model level will retain any specific on/off settings, e.g. if you had only specific ones hidden and others shown.
hide @ca pseudobonds
... would hide all pseudobonds between CA atoms, leaving any others shown (h-bonds, metal coordination, etc.).
You could also close it
close #1.1
...but then it could automatically regenerate if you are showing CA atoms but not the other backbone atoms between them.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 16, 2020, at 3:19 PM, Derek Harris <derek.harris@aggiemail.usu.edu> wrote:
Hello,
When I hide the backbone and choose to show side chain and base any sequential residues shown have a small line between the CA's. I can select them, but not delete them or hide them as an atom or bond, only hide sel, but when the selection they are a part of is hidden and reshown they reappear. I can also assign them as a selector and hide/show them, but also as soon as I hide and reshow the selection they are a part of they reappear and the designated selector for them is gone from the list.
I want to retain the side chain and base appearance but lose these lines permanently. Any help would be appreciated.
Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Derek Harris -
Elaine Meng -
Tom Goddard