[phenixbb] refinement for ligands with alternative conformation

Pavel Afonine pafonine at lbl.gov
Mon Mar 21 21:35:13 PDT 2011


unless I'm missing something, I think there is no need to use insertion 
code... All you need is to:

1) edit your PDB file to add altloc identifiers to individual components,
2) make sure the whole thing has the same residue number and chain id 
(example: see residue number 22 here http://www.rcsb.org/pdb/files/1EJG.pdb)
3) either go by the automatic grouping of occupancies (=do nothing, run 
phenix.refine), or instruct phenix.refine how it should combine 
individual conformers using

occupancies {
   constrained_group {
      selection = ..

as described here:

If still confused, then send me a PDB file with the extract of residues 
in question and tell me how they are expected to be grouped and I will 
send you back an example.


On 3/21/11 8:48 AM, Nathaniel Echols wrote:
> On Mon, Mar 21, 2011 at 6:35 AM,<zhengyi at msu.edu>  wrote:
>> I am working on the refinement of a structure about 2.8A, which the
>> substrate ligand has an odd conformation. A blob of negative difference
>> density about 4.8 sigma between the one portion of the ligand and the other.
>> If I break down the ligand into two parts, the negative density disappears,
>> however, one part of the ligands does not fit well. We suspect a mixture of
>> conformations.
>> Any suggestions would be appreciated on how to setup refinement for ligands
>> with alternative conformation.
> In theory it's just like setting up alternate conformations for
> protein residues.  However, it sounds like you have something similar
> to a partially hydrolyzed ATP, where conformation "A" is ATP, and
> conformation "B" is ADP (perhaps in combination with phosphate).
> There is nothing in phenix.refine that prevents you from doing this -
> unfortunately, it probably requires editing the PDB file manually to
> create the alternate conformations and rename the altloc (the column
> to the left of the residue name).  For the other half of the
> hydrolyzed ligand, if you decide to model this explicitly, I'd
> recommend using the insertion code (the column to the right of the
> residue number), and leaving the residue number the same.  Thus for
> ATP+ADP+Pi, you would end up with:
> ATP = conformer A, residue 1
> ADP = conformer B, residue 1
> Pi = conformer B, residue 1P
> Messy, but it should work.
> -Nat
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