Re: [chimerax-users] [Chimera-users] interface plot
Oops, I meant to send this to chimerax-users@cgl.ucsf.edu , not chimera-users@cgl.ucsf.edu (apologies to the latter folks)! Elaine
On May 12, 2022, at 12:27 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Pranav, If you mean that you wanted a list of the interface residues, you can use the "interfaces" network diagram edge context menu to select the residues, then list them in the Log with "info residues sel" ... and either cut-n-paste from the Log to text file or use "log save" to save it as an HTML file. The "info" command should really allow saving a text file directly, but it doesn't do that yet. I believe we have an open ticket to fix that omission.
In the chain-chain network diagram, e.g. when the mouse cursor is over the edge representing the chain B-C interface, context-menu choices include
Select Contact Residues of B and C Select Contact Residues of B with C Select Contact Residues of C with B
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#diagram>
Or if you get a new daily build, another way to select the residues is to use menu: Select... Contacts, the Chains section of the resulting dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>
Then use "info residues sel" and possibly "log save" as mentioned above. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save>
Alternatively, you could use "measure buriedarea" specifying the two chains and "list true", which also reports each residue's buried area. (thus avoiding having to select and use "info") <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea>
Example: measure buriedarea (/A&protein) with (/B&protein) list true
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 12, 2022, at 9:06 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Indeed! Although, as a suggestion, would it be possible to highlight in the description that in order for the plot to inherit residue colors, one needs to invoke the plot _after_ the residues have been identified and colored? Also, could I save the output of the analysis to a text file? 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 Thu, May 12, 2022 at 4:53 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
haha, glad you like it!!
Best, Elaine
On May 12, 2022, at 8:27 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
<3 <3 <3 <3 <3
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 <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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Thanks! That helps! 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 Thu, May 12, 2022 at 8:47 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Oops, I meant to send this to chimerax-users@cgl.ucsf.edu , not chimera-users@cgl.ucsf.edu (apologies to the latter folks)!
Elaine
On May 12, 2022, at 12:27 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Pranav, If you mean that you wanted a list of the interface residues, you can use the "interfaces" network diagram edge context menu to select the residues, then list them in the Log with "info residues sel" ... and either cut-n-paste from the Log to text file or use "log save" to save it as an HTML file. The "info" command should really allow saving a text file directly, but it doesn't do that yet. I believe we have an open ticket to fix that omission.
In the chain-chain network diagram, e.g. when the mouse cursor is over the edge representing the chain B-C interface, context-menu choices include
Select Contact Residues of B and C Select Contact Residues of B with C Select Contact Residues of C with B
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#diagram>
Or if you get a new daily build, another way to select the residues is to use menu: Select... Contacts, the Chains section of the resulting dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>
Then use "info residues sel" and possibly "log save" as mentioned above. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save>
Alternatively, you could use "measure buriedarea" specifying the two chains and "list true", which also reports each residue's buried area. (thus avoiding having to select and use "info") <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea>
Example: measure buriedarea (/A&protein) with (/B&protein) list true
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 12, 2022, at 9:06 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Indeed! Although, as a suggestion, would it be possible to highlight in the description that in order for the plot to inherit residue colors, one needs to invoke the plot _after_ the residues have been identified and colored? Also, could I save the output of the analysis to a text file? 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 Thu, May 12, 2022 at 4:53 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
haha, glad you like it!!
Best, Elaine
On May 12, 2022, at 8:27 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
<3 <3 <3 <3 <3
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 <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, Short of taking a screenshot of the plot, is there a way to save said plot via the command line? 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 Fri, May 13, 2022 at 9:06 AM Pranav Shah <p.shah.lab@gmail.com> wrote:
Thanks! That helps! 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 Thu, May 12, 2022 at 8:47 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Oops, I meant to send this to chimerax-users@cgl.ucsf.edu , not chimera-users@cgl.ucsf.edu (apologies to the latter folks)!
Elaine
On May 12, 2022, at 12:27 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi Pranav, If you mean that you wanted a list of the interface residues, you can use the "interfaces" network diagram edge context menu to select the residues, then list them in the Log with "info residues sel" ... and either cut-n-paste from the Log to text file or use "log save" to save it as an HTML file. The "info" command should really allow saving a text file directly, but it doesn't do that yet. I believe we have an open ticket to fix that omission.
In the chain-chain network diagram, e.g. when the mouse cursor is over the edge representing the chain B-C interface, context-menu choices include
Select Contact Residues of B and C Select Contact Residues of B with C Select Contact Residues of C with B
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#diagram>
Or if you get a new daily build, another way to select the residues is to use menu: Select... Contacts, the Chains section of the resulting dialog: <https://rbvi.ucsf.edu/chimerax/docs/user/selectcontacts.html>
Then use "info residues sel" and possibly "log save" as mentioned above. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#save>
Alternatively, you could use "measure buriedarea" specifying the two chains and "list true", which also reports each residue's buried area. (thus avoiding having to select and use "info") <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea>
Example: measure buriedarea (/A&protein) with (/B&protein) list true
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 12, 2022, at 9:06 AM, Pranav Shah <p.shah.lab@gmail.com> wrote:
Indeed! Although, as a suggestion, would it be possible to highlight in the description that in order for the plot to inherit residue colors, one needs to invoke the plot _after_ the residues have been identified and colored? Also, could I save the output of the analysis to a text file? 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 Thu, May 12, 2022 at 4:53 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
haha, glad you like it!!
Best, Elaine
On May 12, 2022, at 8:27 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
<3 <3 <3 <3 <3
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 <image.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users
Hi Pranav, Sorry no, as far as I know there's no built-in way to save images of these plots from the "interfaces" command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 17, 2022, at 1:54 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Short of taking a screenshot of the plot, is there a way to save said plot via the command line? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
Hi Pranav, I've added a "Save Plot As..." menu entry to the interfaces chain and residues plot. Click on those plots to show the menu. The plot can be saved as a PNG image, or SVG (scalable vector graphics), or PDF format file. This will be in tonight's ChimeraX builds that will eventually become ChimeraX 1.5 (not in 1.4). Tom
On May 17, 2022, at 9:26 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav, Sorry no, as far as I know there's no built-in way to save images of these plots from the "interfaces" command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 17, 2022, at 1:54 AM, Pranav Shah via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Short of taking a screenshot of the plot, is there a way to save said plot via the command line? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Awesome, thanks! On Wed, 18 May 2022 at 04:45 Tom Goddard <goddard@sonic.net> wrote:
Hi Pranav,
I've added a "Save Plot As..." menu entry to the interfaces chain and residues plot. Click on those plots to show the menu. The plot can be saved as a PNG image, or SVG (scalable vector graphics), or PDF format file. This will be in tonight's ChimeraX builds that will eventually become ChimeraX 1.5 (not in 1.4).
Tom
On May 17, 2022, at 9:26 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Pranav, Sorry no, as far as I know there's no built-in way to save images of these plots from the "interfaces" command. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 17, 2022, at 1:54 AM, Pranav Shah via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine, Short of taking a screenshot of the plot, is there a way to save said plot via the command line? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow.
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- 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
participants (3)
-
Elaine Meng -
Pranav Shah -
Tom Goddard