I fitted manually the chondroitin sulfate into my complex (3c9e.pdb and 3h7d)
using program coot. The chondroitin-sulfate model was used from the PDB. I used
CNS for the refinement of the first structure, and phenix for the second
structure. Phenix was more convenient with this ligand as it was a polymer
chain running through many unit cells. What sulfated sugar did you use? How big
it is?
Maia
----- Original Message -----
From: Vandu Murugan
To: CCP4BB@JISCMAIL.AC.UK
Sent: Friday, July 30, 2010 5:28 AM
Subject: [ccp4bb] MR with polysaccharide
Dear all,
I am seeing some bulk extra denisty near my protein molecule, in a 2.7
angstrom map. The crystallization condition condition has a sulfated
polysaccharide. If I want to perform a MR with this polysaccharide, in
presence of the refined protein model in the cell, which program should I use?.
In the phaser, there are options only for proteins and nucleic acids. Is
there, any automated ligand identifying/fitting program that can work at this
resolution? All suggestions are wellcome. Thanks in advance.
warm regards,
Murugan
