Bugs item #1027413, was opened at 2004-09-13 13:16 Message generated for change (Settings changed) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1027413&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Deleted >Resolution: Works For Me Priority: 5 Submitted By: Miguel (migueljmol) Assigned to: Miguel (migueljmol) Summary: CONECT & LINK Initial Comment: Figure out what the proper relationship is between CONECT records and LINK records in .pdb files ---------------------------- Original Message ---------------------------- Subject: [Jmol-developers] CONECT and LINK From: "Jan Reichert" <[EMAIL PROTECTED]> Date: Thu, September 9, 2004 10:43 To: [email protected] Cc: "G. Jawahar Swaminathan" <[EMAIL PROTECTED]> -------------------------------------------------------------------------- I had asked RCSB for correction of 1hc8 CONECT records and learned that there is a link to LINK :-) It was because of strange bonds in Jmol with 1hc8: http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1hc8 LINK MG MG C1166 O4 U D 358 1555 7556 HETATM 2328 MG MG C1166 121.733 89.904 19.310 1.00 55.88 ATOM 3583 O4 U D 358 88.821 122.743 46.618 1.00 76.28 CONECT 3583 2328 CONECT 2328 3583 The LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. This record supplements information given in CONECT records and is provided here for convenience in searching. from: http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_48.html I cite Jawahar Swaminathan: >The two numbers shown above 1555, 7556 indicate the nature of connections between >the ION and protein residues. These numbers indicate the symmetry operators which are necessary to make the connection. These values are derived from Remark 290 of the PDB file and have the following format: > >1555 : Symmetry operator for the first atom, where this is sym 1 of rem290 > >REMARK 290 1555 X,Y,Z and 555 indicate no translation. This means that MG C1166 is from the deposited coordinate set. > >7556: Symmetry operator of the second atom (O4 of U D358). > >where 7 is sym.op Y,X,-Z from rem290 > >556 - no translation along Y, X but translation of 1 along Z. > >So essentially this LINK record is between MG from the deposited coordinate and O4 of a symmetry-related O4 (operator 7556). The CONNECT records shown in the PDB file need to be seen in conjunction with these LINKs. > >Unfortunately, many PDB viewers do not make use of this information, with the result that the bonds can appear to be extremely long connecting across long distances. > >I hope this helps. > >best regards, > >Jawahar Swaminathan >PDB Depositions and suggest Jmol should consider the LINK information, especially because Jmol will support symmetry operations in a later stage. With kind regards, Jan ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1027413&group_id=23629 ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
