[Chimera-users] LINK record not honoured in Chimera?

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 4 16:35:45 PST 2020

Hi Kate,
An example is 1F88 (rhodopsin) where there is both a LINK record and a CONECT record for the bond between lysine NZ and the retinal chromophore.  Excerpted lines from that PDB file:

LINK         NZ  LYS A 296                 C15 RET A 977     1555   1555  1.46

ATOM   2321  NZ  LYS A 296      51.283  12.449  -8.206  1.00 26.12           N

HETATM 5145  C15 RET A 977      52.545  11.720  -8.232  1.00 25.08           C

CONECT 2321 5145

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 4, 2020, at 4:22 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 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 at 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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