Lijun Liu 's suggestion is sensible.   And is there any possibility of 
twinning? 

But I always thought that at least in REFMAC all A conformations were 
restrained as a set, and ditto for B C etc.

So if the documentation is to be believed an A chain  would be restrained as a 
unit. I don't think there is any way to force the occs of the A ligand and A 
chain to refine together but at 2.5A you wouldn't want to refine occs anyway I 
guess. 
Eleanor

 
On 7 Aug 2012, at 19:22, Dale Tronrud wrote:

>   You have to build the model you actually believe matches what is in
> the crystal.  Do you believe that each amino acid is occupying two
> conformations independent of its neighbors?  I wouldn't go that way.
> I would start with an apo conformation, labeled with 'g', and a holo
> conformation including the ligand, labeled with 'h', and allow all of
> 'g's one occupancy value, and the 'h's another, and insist that they
> sum to 1.0.  You may have to build water molecules in the binding site
> of 'g' that are displaced by the ligand in 'h'.
> 
>   If this, simplest of models, doesn't do the trick you have to be
> lead by your difference maps and chemical intuition to devise more
> complex models.  Select the simplest model that makes sense and fits
> your data.
> 
>   It would be interesting to see if you can find a program that would
> allow you to restrain the ncs of the second protein chain and the 'h'
> conformation of your mixed model, leaving the 'g' conformation unrestrained
> by ncs.
> 
> Dale Tronrud
> 
> P.S. I'm avoiding the use of 'A' and 'B' alt locs because these are
> routinely used when splitting side chains but are almost never intended
> to imply that all 'A's are coordinated with each other and all 'B's are
> likewise.  To be proper, the reuse of alt loc codes for unrelated
> conformations should not be allowed, but there are simply not enough
> letters to allow the rule to be enforced.
> 
> On 08/07/12 07:59, Kendall Nettles wrote:
>> Hi,
>> We have a structure with the ligand showing two overlapping conformers.
>> When we refine it with both conformers separately, it is pretty clear
>> that there are substantial differences in the protein as a result, for
>> about a third of the protein chain. My question is, would it be better
>> to try to define alternate conformers for those specific regions, or
>> would it be OK to refine with two entire alternate protein chains? There
>> is also a second protein chain that shows only a single binding mode for
>> the ligand.  It's a 2.0 angstrom structure. The yellow 2Fo-Fc map goes
>> with the green model in the attached pic. Also, do we want to let each
>> amino acid have its own occupancy? or should one ligand copy and one
>> chain all have the same occupancy? I'm leaning towards the latter since
>> the differences should be directly tied to the ligand binding mode. 
>> Kendall Nettles

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