Hi,
if you feel you are good at _chem_link sections of dictionary files (and know
how refmac understands them), please read on.
My question in short:
what is the Right Way of defining a covalent link between a ligand that is not
in the standard refmac library and a standard amino acid residue, using
_chem_link?
Longer version:
I have a series of ligands binding covalently to the same residue with the same
geometry, therefore it seems reasonable to define a link for all of them (and
use that as an invariant part of the description of the ligands and their bond
to the protein). [1]
I've generated _chem_link and _chem_comp descriptions, merged them in one cif
file and wrote a LINK card in the pdb file. The ligand description corresponds
to the one in the bound state so no _chem_mod should be required. Still,
haven't had much luck with refmac:
1. if the _chem_link section precedes the _chem_comp part in the cif file:
refmac doesn't seem to recognise the ligand and fails.
2. if the _chem_comp part comes first in the cif file, refmac fails with
"CYS-INH not found in the list of links" (where CYS-INH is the _chem_link I
defined).
3. if the _chem_link_list and _chem_comp_list precede the actual
descriptions in the file, refmac simply ignores the link part, which in turn
results in a distorted geometry of the ligand-protein bond. There's no warning
about unrecognised links in the log file.
What am I missing here?
Any suggestion most welcome.
JED
[1] I could simply treat the ligand and amino acid residue as one single unit,
but computational chemists would like to see them as separate entities, so
refining them together (i.e. as a modified amino acid) is not an option. Not
very straight forward, anyway.
Defining one ligand as starting point and generate the others with _chem_mod is
somewhat tedious to script, so I dropped that option too.
--------------------------------------------------------------------------
AstraZeneca UK Limited is a company incorporated in England and Wales with
registered number: 03674842 and a registered office at 15 Stanhope Gate, London
W1K 1LN.
Confidentiality Notice: This message is private and confidential and may
contain confidential, proprietary and legally privileged information. If you
have received this message in error, please notify us and remove it from your
system and note that you must not copy, distribute or take any action in
reliance on it. Any unauthorised use or disclosure of the contents of this
message is not permitted and may be unlawful.
Disclaimer: Email messages may be subject to delays, interception, non-delivery
and unauthorised alterations. Therefore, information expressed in this message
is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by
an authorised representative independent of this message. No contractual
relationship is created by this message by any person unless specifically
indicated by agreement in writing other than email.
Monitoring: AstraZeneca UK Limited may monitor email traffic data and content
for the purposes of the prevention and detection of crime, ensuring the
security of our computer systems and checking Compliance with our Code of
Conduct and Policies.
