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 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

***********************************

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]