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

[Greg Couch]

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 at cgl.ucsf.edu 
> <mailto:meng at 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 at cgl.ucsf.edu
>     <mailto: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
>     <mailto: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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