On 28/10/10 20:12, Changyi Xue wrote:
Hi, all
I am trying to build an oligomer ligand. I have obtained all the
cif files for the monomers from HIC-UP. I tried to build several
monomers in using coot. Then I modified the pdb file and stated the
link in the pdb head (LINKR X ABC 1 Y ABC 2 X-Y).
However, when using refmac to refine, it always separated the monomers
and broke the bond, which I could fix it back in coot using 'real
space refine zone'.
I am wondering, what is the general practice to build such oligomer
ligand?
Having a LINK in the PDB will show the link in the graphics.
Having a link description in the cif file will allow you to refine it
(presuming that such a link is not already in the dictionary). This
applies to any refinement program. If you want to refine the link with
Coot, you will need to use "Sphere Refinement". (IMHO) cif link
descriptions are not straightforward (not for the first few times that
you make one, that is).
Paul.
