Hi Kate, If the connectivity of the DCR residue is specified in CONECT records (which it probably is), you may have to add a CONECT record (or add to the existing CONECT record for the DCR carbonyl carbon) specifying the bond you want. If the LINK were between standard residues (which don’t have CONECT records), then I believe the LINK by itself would work. One other thing to do is to look at the reply log (Favorites→Reply Log) and see if there are any complaints when you open the file. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Mar 4, 2020, at 4:03 PM, Kate Kim <kimsk@msg.ucsf.edu> wrote:
Hello,
I would like to visualize a thioester bond between a CYS residue of my protein and a carbonyl carbon of ligand (DCR) in my model.
I have a LINK record for the DCR-CYS thioester bond created from Jligand and inserted in the PDB right before the CRYST1 line.
However, when I open this PDB in Chimera, the thioester linkage is not drawn. The distance between the C1 of DCR and SG of CYS is 1.79 angstrom.
Does Chimera need something else other than the LINK record in the PDB to display the bond?
Thank you, Kate
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