Re: [ccp4bb] refining large region with multiple conformers

[Dale Tronrud]

   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

Re: [ccp4bb] refining large region with multiple conformers

[Lijun Liu]

Hi,

~1/3 of a chain that show substantial difference suggests a  
possibility that may deserve a check---the symmetry is actually lower  
and the 2 conformations belong to two occ=1 mols (unless the SG is  
already P1).


I had a case that the apo SG was P1 and ligand-bound (soaked) SG was  
P1 too but the binding made the data very well reducible to P2.  When  
refined with P2, I got something like you mentioned.  When going back  
with P1, everything turned to be clean, also R and Rfree were ~3% lower.



Lijun



On Aug 7, 2012, at 9:59 AM, 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
coot.png