[chimerax-users] protein-protein interacting footprints

[Krishnan Raman]

Hi Elaine,
Thanks😊  and have a happy thanksgiving.
Regards
Krish

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

From: Elaine Meng<mailto:meng at cgl.ucsf.edu>
Sent: Monday, November 21, 2022 1:43 PM
To: Krishnan Raman<mailto:RKrishnan at BIOCRYST.com>
Cc: ChimeraX Users Help<mailto:chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] protein-protein interacting footprints

[EXTERNAL]

Hi Krish,
Generally it would be in two steps: select interface, then apply action (e.g. coloring) to what was selected.

Commands for identifying interface by various methods:

(1) interfaces - chain-chain interfaces based on buried surface area, also draws diagrams with context menus for selecting the atoms involved
<https://link.edgepilot.com/s/2b888668/z1ykJlP3oEq-Vl8yudq9mQ?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>

(2) contacts - pairwise atomic interactions identified by VDW overlap (i.e. 0 for touching VDW surfaces, positive for intersecting VDW surfaces; typically use negative value to include atoms that are almost touching), or by a simple center-to-center cutoff distance; includes option to select identified atoms
<https://link.edgepilot.com/s/b61f5f32/pYIRVPHR00a8sQ8yeN4DhA?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>

(3) a third approach is to just use a zone specification in the command (e.g. color, select, etc.), which uses a simple distance cutoff.  For example, to color red all atoms/ribbons/surfaces of protein residues in chain A with any atom within 3.8 angstroms of any protein residue in chain B:

color (/A & protein) & (( /B & protein) :<3.8) red target ars

...or for atom-based (could be partial residues colored rather than whole residues)

color (/A & protein) & (( /B & protein) @<3.8) yellow target ars

Of course you would have to additionally display the atoms to see their coloring.  Or you can select and color in separate steps,

select (/A & protein) & (( /B & protein) @<3.8)
color sel hot pink target ars

<https://link.edgepilot.com/s/fb4dbf3f/DnbzhC5A5UiKDdUIclPkig?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html%23new>
<https://link.edgepilot.com/s/59543046/YP1kcu6u4ECfDiorxYGkew?u=https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html%23simple>

There is no specific recommendation for 3.8, it's just there to show you that you can put in whatever distance you like.  Or, if you want to factor in the different VDW radii of atoms, you would use the "contacts" command instead.

The menu entries: Select... Zone, Select... Contacts use these three methods depending on what options you choose, so you may want to try experimenting with that interactively to see what commands they generate, which will be shown in the Log.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 21, 2022, at 9:44 AM, Krishnan Raman via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Hi
> Can you please point me to
> Commands for calculating/coloring the interacting  interfaces (surfaces, atoms) for protein-protein interactions in chimerax?
> Thanks
> Krish



Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning.


CONFIDENTIALITY NOTICE

This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20221121/9b134b33/attachment.html>