[phenixbb] Coupling ligand occupancy with helix displacement

Oleg Sobolev osobolev at lbl.gov
Mon Jun 11 10:36:31 PDT 2018


Hi John,

Why don't you make 3 alternative conformations for helix 589:598 as well?
In this case you would define constrained_group with 3 selections, very
much like in the example 7 you are referring to.

Best regards,
Oleg Sobolev.

On Wed, Jun 6, 2018 at 11:06 AM, John Michael Bruning <bruning at stanford.edu>
wrote:

> Hi,
>
>
> I have a very flexible covalent adduct that adopts three alternative
> conformations (A,B,C) in my structure . Conformations A and C are solvent
> exposed, while conformation B is buried. The buried conformation B
> displaces a regulatory helix (resseq 589:598) by a few angstrom, while the
> solvent exposed conformations do not displace this helix. I can't seem to
> write a occupancy .params file that fulfills:
>
>
> 1.) occ. of ligand conformation B = occ. of displaced helix conformation #
> coupling of ligand binding with helix displacement
>
> 2.) occ. non-displaced helix conformation = (1 - occ. displaced helix
> conformation)
>
> 3.) sum occ. ligand conformations A+B+C = 1 # assuming protein was
> initially labeled 100%
>
>
>
> It seems like #7 from http://www.phenix-online.org/
> newsletter/CCN_2015_07.pdf#page=12 is my situation, but I can't quite
> seem to modify this for my case. For example, something like:
>
>
> constrained_group {
>                 selection = chain A and resname CPE and altid B or chain A
> and resseq 589:598 and altid B}
>
>
> Captures the concerted conformation aspect (1) (occupancy for ligand
> conformation B = occupancy for displaced helix) and the sum occupancy of
> the displaced and non-displaced helix = 1 (2), but the sum of the the
> alternative conformations A+B+C > 1.0 (w/ A+C = 1.0) (3)
>
>
> Incidentally, my resolution is 2.4 Ang. Thanks for any help!
>
>
> Cheers,
>
>  John
>
>
> Cheers,
>
>  John
>
>
> ***********************************
>
> John Bruning, Post-Doctoral Scholar
>
> Stanford University, Glenn Lab
>
> CCSR Building, #3110
>
> ***********************************
>
>
>
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