[Chimera-users] [chimerax-users] interface plot

[Elaine Meng]

Oops, I meant to send this to chimerax-users at cgl.ucsf.edu , not chimera-users at cgl.ucsf.edu (apologies to the latter folks)!

Elaine

> On May 12, 2022, at 12:27 PM, Elaine Meng via Chimera-users <chimera-users at 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 at 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 at 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 at 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
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> 
> 
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