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 ----- 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@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@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

Remove the trailing DCR-CYS in your LINK records, they are illegal.  If you look at the PDB's 1F88's LINK records, they are of the form: LINK         C1  NAG B 602                 O4  NAG B 601 1555   1555  1.38 LINK         C1  NAG B 802                 O4  NAG B 801 1555   1555  1.39 So where you have DCR-CYS, Chimera is expecting a numerical symmetry operator.  The PDB format specification is published at http://www.wwpdb.org/documentation/file-format.  In general, for PDB files, not specifying something, rather than putting in "random" characters, works better.     Good luck,     Greg On 3/4/2020 6:36 PM, Kate Kim wrote:

Hi Elaine and Eric,

Thank you for your reply.

I tried to follow the example of 1F88, and I have:

LINK         C1  DCR A 1101            SG  CYS A 267          DCR-CYS LINK         C1  DCR B 1201            SG  CYS B 267      DCR-CYS ATOM   7896  SG  CYS B 267     149.139 168.091 151.319  1.00 24.38           S ATOM   1371  SG  CYS A 267     174.729 167.809 164.051  1.00 27.17           S HETATM 6472  C1  DCR A1101     174.148 169.497 163.870  1.00 30.17           C HETATM12696  C1  DCR B1201     148.862 169.613 152.232  1.00 29.68           C CONECT 1371 6472 CONECT 7896 12696

The log says, warning: Ignored bad PDB record found on line 148 warning: Ignored bad PDB record found on line 149

Lines 148 & 149 refer to the two LINK records. Why is it saying that it is bad? Does my LINK record (obtained from Jligand) need to be altered for Chimera?

Thank you.

On Wed, Mar 4, 2020 at 4:35 PM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:

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 ----- 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@cgl.ucsf.edu <mailto:pett@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@msg.ucsf.edu <mailto: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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