Well, it is not based on residue numbering. A possible way to deal with this ould be to parse the pdb information in LINK records. Henry's file (2HK4.pdb) has them: LINK P C A 1 O3* T A 8 LINK P C B 1 O3* T B 8
They are meant to supplement info in CONECT records, and to be used for: 1. Bonds between HET groups or between a HET group and standard residue, 2. Inter-residue linkages not implied by the primary structure 3. etc. Point 2 looks to me like the current case. Point 1 would also be interesting (not sure now whether Jmol currently links hetgroups and residues in cartoons, will check) This is the PDB spec: ·························· The LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. [snip] Record Format COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------- 1 - 6 Record name "LINK " 13 - 16 Atom name1 Atom name. 17 Character altLoc1 Alternate location indicator. 18 - 20 Residue name resName1 Residue name. 22 Character chainID1 Chain identifier. 23 - 26 Integer resSeq1 Residue sequence number. 27 AChar iCode1 Insertion code. 43 - 46 Atom name2 Atom name. 47 Character altLoc2 Alternate location indicator. 48 - 50 Residue name resName2 Residue name. 52 Character chainID2 Chain identifier. 53 - 56 Integer resSeq2 Residue sequence number. 57 AChar iCode2 Insertion code. 60 - 65 SymOP sym1 Symmetry operator atom 1. 67 - 72 SymOP sym2 Symmetry operator atom 2. 74 - 78 Real(5.2) Length Link distance ·························· ------------------------------------------------------------------------------ This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
