[Chimera-users] LINK record not honoured in Chimera?
gregc at cgl.ucsf.edu
Wed Mar 4 23:00:24 PST 2020
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.
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
> ATOM 1371 SG CYS A 267 174.729 167.809 164.051 1.00 27.17
> HETATM 6472 C1 DCR A1101 174.148 169.497 163.870 1.00 30.17
> HETATM12696 C1 DCR B1201 148.862 169.613 152.232 1.00 29.68
> 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 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
> >> 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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