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Judit, Refmac does seem to be very picky about the order. See attached file in which I had to add several links; this file works, so a few minutes of reverse engineering on your part should make it clear what you need to do in what order. Hope this helps, Dave David Borhani, Ph.D. D. E. Shaw Research, LLC 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 [log in to unmask] 212-478-0698 http://www.deshawresearch.com > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On > Behalf Of Debreczeni, Judit > Sent: Friday, November 21, 2008 7:19 AM > To: [log in to unmask] > Subject: [ccp4bb] bespoke _chem_link in refmac > > 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. >