[Chimera-users] interface residues
meng at cgl.ucsf.edu
Mon Mar 17 15:27:02 PDT 2008
On Mar 17, 2008, at 9:56 AM, Francesco Malatesta wrote:
> could anyone help me out with this problem. I would like to
> exclusively colour interface residues in a dimeric protein
> represented as spheres or surface. Is this possible?
> Thank you very much
> Francesco Malatesta
Of course - there are so many different ways you could do it, I'm not
sure where to start! Also, I don't know if your structure is opened
from two PDB files, or one PDB file with a different chain ID for
each monomer. You could do it either way, but in my examples I will
assume you have one file with protein chains A and B like structure
1tzz. My examples are commands, but the same things can be done with
menus and/or graphical interfaces (it would just take a lot more
words to describe).
Possible ways to identify the residues:
(a) with a simple distance cutoff (Select... Zone... or in commands)
color red :.a & :.b za<5
- that would color atoms in chain A that are within 5 angstroms of
any atom in chain B; you can include a distance limit in many other
commands, such as "select" "display" "repr sphere" "surface" etc.
The "za" means atom-based cutoff, whereas "z" or "zr" means residue-
based (would color whole residues with any atom within that
distance). You would then use a similar command for atoms in chain B
close to atoms in chain A.
(b) with Find Clashes/Contacts (under Tools... Structure Analysis) or
findclash :.a overlap -0.5 hb 0 makePseudobonds false select true
~select ~ :.b
- the first command selects any atoms outside of chain A that are
close to chain A (any atoms with VDW surfaces within 0.5 angstroms of
the VDW surfaces of atoms in chain A). The second command deselects
atoms NOT in chain B, so what you have left are just the atoms in B
that are close to A. Then you can do what you want to the selected
atoms with the Actions menu or other commands (including writing out
a list of the atoms or residues). Next, use similar steps to get
atoms in chain A that are close to the atoms in chain B.
(c) with Intersurf (under Tools... Surface/Binding Analysis) or
intersurf :.a :.b select true prune 10
That would select all the atoms from both chains found to form the
interface. See the links above for the algorithm. The "prune"
distance controls how far out to the sides the interface is computed
and thus how many atoms will be selected. Intersurf creates a
special interface surface and opens a dialog for recoloring it based
on the distances between the subunits. If you don't want that
surface, you can just close it.
One other thing I should mention is that sometimes "surface" (display
molecular surface, which is different than the special "intersurf"
surfaces) will enclose multiple chains in the same surface when
instead you wanted a separate surface for each chain. You can tell
Chimera to make separate surfaces, as explained here:
I hope this helps,
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
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