Briefly (and top-postingly), Coot does not draw covalent bonds between non-tandem residues.
Coot will represent LINK records if they are in the PDB file. Coot will respect the links generated by JLigand if you try to do sphere refinement. The Coot <--> JLigand internface will improve in the not too distant future. Paul. ________________________________________ From: CCP4 bulletin board [[email protected]] On Behalf Of Tim Gruene [[email protected]] Sent: 08 June 2010 21:04 To: [email protected] Subject: Re: [ccp4bb] JLigand Coot link 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? > -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
