Tim, Garib, Sorry, maybe I'm missing something here but how does the user specify that (s)he wants a TRANS link between standard amino-acids (ASN-GLY) in this case? Isn't that the default? I always thought the answer was to add a LINK record for those two residues in the PDB file using the format specified in the PDB guide, e.g.
LINK C ASN B 729 N GLY B 741 (or just paste the LINKR record from the output PDB file and change LINKR to 'LINK '). But this raises an important issue. The PDB entries contain many examples of this, i.e. where there's a gap in the numbering but not in the sequence, and the PDB guide on the LINK record states: "The LINK records specify connectivity between residues *that is not implied by the primary structure*." (my emphasis). My reading of this is that it's the primary structure (i.e. the SEQRES records) that specify that the residues are contiguous, *not* the residue numbering. Perhaps someone from one of the PDB deposition sites could comment and verify my reading of this? If this is the case then Refmac is ignoring a perfectly valid PDB format, and requiring that the user supplies a non-agreed format! - but of course I could be wrong in my interpretation (in which case of course I withdraw from the argument!). But if I'm right then it seems to me that refinement programs should at the very minimum be able to treat completely valid PDB entries correctly, and not require the user to make non-standard changes. Cheers -- Ian > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Garib Murshudov > Sent: 16 August 2009 22:09 > To: Tim Fenn > Cc: [email protected] > Subject: Re: [ccp4bb] LINKR in refmac > > Tim is right. The link you want is TRANS. And if you want link between > alternative position then you need to add alt codes before residue names. > Llink ids must be defined in the dictionary. There are definitions for > standard links in the dictionary: $CLIBD_MON/list/mon_lib_list.cif. > > For templates how to use various forms of links please have a look: > http://www.ysbl.york.ac.uk/refmac/data/template_link.txt > > If you experience further difficulties please let me know and I will try > to sort this out. > > regards > Garib > > > > 2009/8/14 Tim Fenn <[email protected]> > > > On Fri, 14 Aug 2009 13:24:16 -0700 > Jan Abendroth <[email protected]> wrote: > > > How can I tell refmac to maintain the peptide link? > > Here is what I tried - the numbers above just for orientation > > > > 1 2 3 4 5 6 > > 7 8 > > > 123456789012345678901234567890123456789012345678901234567890123456789012 34 > 567890 > > LINKR C ASN B 729 N GLY B 741 ASN-GLY > > > > refmac comments in the log file ... however, still pulls the > residues > > apart. WARNING : description of link:ASN-GLY is not in the > dictionary > > link will be created with bond_lenth = 1.260 > > > > So, in my understanding it comes down to the question: > > how is a peptide bond referenced to in the dictionary? > > > > > take a look at the data_link_list loop in mon_lib_list.cif (there > may > be an easier way to view this info): > > TRANS . . peptide . . peptide > default-peptide-link > PTRANS . . peptide PRO . . > default-peptide-link_pro > NMTRANS . . peptide PRO . . > default-peptide-link_cn > CIS . . peptide . . peptide > cis-peptide-link > PCIS . . peptide PRO . . > cis-peptide-link_pro > NMCIS . . peptide PRO . . > cis-peptide-link_cn > > > so you probably want TRANS. > > HTH, > Tim > > -- > --------------------------------------------------------- > > Tim Fenn > [email protected] > Stanford University, School of Medicine > James H. Clark Center > 318 Campus Drive, Room E300 > Stanford, CA 94305-5432 > Phone: (650) 736-1714 > FAX: (650) 736-1961 > > --------------------------------------------------------- > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [email protected] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
