Hi Sean, do the ligand and the Thr belong to the same chain, and did you check that the distance between the bonding atoms is not beyond coot's cut-off?
Tim On Tue, Jun 08, 2010 at 11:16:03AM -0700, Sean Gay wrote: > I have used JLigand v 0.2.1 to create a link between a Thr residues and > a covalent adduct. The adduct refines well and shows up as a covalent > bond in PyMOL. However, when I'm in Coot there is no bond present > between the Thr OG1 and the ligand. I've loaded the Jligand link.lib > file that I created and the cif for the ligand itself into Coot. Any > ideas how to fix this? > > Sean > > Sean C. Gay, PhD > Postdoctoral Scholar > Skaggs School of Pharmacy and Pharmaceutical Sciences > University of California, San Diego > 9500 Gilman Dr. #0703 > La Jolla, CA 92093 > Tel. (858)822-7804 > Fax. (858)246-0089 > Email. [email protected] -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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