Baldeep,
for your covalently modified ligand you may want to specify a LINK
record in the pdb file (see e.g.
http://www.ysbl.york.ac.uk/refmac/data/template_link.txt). Coot should
be able to recognise that and display a bond (i.e. a line between two
atoms, bonds as such are defined in dictionaries by restraints and not
by lines on the screen). JLigand
(http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html) can help you
creating dictionaries for your ligand especially the link ones. These
dictionaries can then be read into Coot:
File->Import Cif Dictionary
for refinement in Coot.
Sorry, no idea how to use these in CNS.
B
I am trying to refine a covalently bound ligand using CNS and coot. The
ligand forms a disulfide bond with the active site Cys residue. I am unable
to see the bond with coot, but I can see it with pymol. I know I need the
.cif files for the restraints to refine the ligand but do I need the
dictionary file to see this covalent bond in coot? If so, where and how do I
input the dictionary file in coot and CNS (generate files?) for refinement?
Thanks,
Baldeep
--
***************************************************
Dr. Bernhard Lohkamp
Assistant Professor
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487673
fax: (+46) 08-327626
email: [email protected]
