Hi Xavier,
In addition to Edward's suggestion, you can have a look at "13 typical
occupancy refinement scenarios and available options in phenix.refine"
article here:
http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12
Scenario #7 looks like your case, but you will have your ligand only in one
conformation.
Best regards,
Oleg Sobolev.
On Tue, Jul 24, 2018 at 8:25 AM, Edward A. Berry
You can make very general alternate conformations with the "constrained_group" construction. Say the loop is N12:14 and ligand is R221 present only in A conformation. You can also add waters to either conformation. The following is for running from .eff script, but I expect it is available from the Gui. There is a detailed description of handling alt conf in one of the newsletters.
refine { occupancies { constrained_group { selection = ((chain N and resseq 12:14) or (chain R and resid 221)) \ and altloc A selection = (chain N and resseq 12:14) and altloc B
}
}} On 07/24/2018 02:49 AM, Xavier Brazzolotto wrote:
I am struggling with a ligand bound structure. The ligand seems to induce a small conformational change of one loop. However, despite my efforts I did not get any data with a full occupancy for this ligand yet.
As a result, I have to deal with a loop in apo state (where ligand occupancy = 0) and a loop with a bound ligand (where ligand occupancy <1) and where the ligand is clashing with the modelled loop in the apo state. Hope I did myself clear.
How to deal with this situation ? I am sure that phenix.refine can do it but how ? What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X Maybe something specific in a parameter file ?
Thank you for your help Xavier
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