[phenixbb] Ligand occupancy and conformational change

[Oleg Sobolev]

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 <BerryE at upstate.edu> wrote:

> 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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