Hi,
I you need to use altLocs to model alternative locations. A good example
is this PDB file (of course there are many more in PDB):
http://www.rcsb.org/pdb/files/1EJG.pdb
see residues #22, 25 etc. Once you have prepared a similar PDB file,
phenix.refine will take of the rest automatically.
Pavel.
On 4/25/10 3:48 PM, Seema Mittal wrote:
Hi All,
I have a structure where electron density shows that the complex
crystallized is not in a unique conformation in the crystal lattice.
It seems the electron density is an average of two possible
orientations of the same complex.
Since, the protein is bound to its substrate as a dimer, where the
sequence of the two monomers (forming the dimer) is different at only
a couple of positions, two different amino acids can be built in the
same electron density. For example, serine vs alanine.
From our previous experience in crystallizing the same complex, we
know that its an averaged density. I am wondering what is the most
accurate and acceptable way to represent it in the actual pdb file
without complicating the analysis.
I am hoping to resolve this issue by getting some inputs from this
expert community.
Thanks in advance,
Best,
Seema Mittal
Graduate Research Assistant,
Department of Biochemistry & Molecular Pharmacology,
970L Lazare Research Building,
University of Massachusetts Medical School,
364 Plantation Street,
Worcester, MA 01605
