Bob Hanson wrote: > OK, well, then, since they messed up there, I highly recommend you use > "connect" just after loading. I've added the test for between-model > bonding in Jmol 11.3.48 > I don't fully trust the connect mechanism in Jmol (I saw for example hydrogen atoms bonded covalently with 2 other atoms in close proximity [a single model file]). Therefore I would prefer to display the "official" bonds.
The PDB format documentation at "http://www.wwpdb.org/documentation/format23/sect10.html"; tells for multiple model cases the following: "For NMR entries, CONECT records for all models are generated describing heterogen connectivity and others for LINK records." This is not really clear. But it becomes more clear in combination with the documentation for "LINK" records at "http://www.wwpdb.org/documentation/format23/sect6.html#LINK": "For NMR entries only one set (or model) of LINK records will be supplied." This means that a single set of "CONECT" records has to be applied to all models (separately). I analyzed the usage of "CONECT" records within all asymmetric and biological unit PDB format files of the Protein Data Bank. The outcome can be summarized as follows: 1) There are never multiple sets of "CONECT" records. (confirming the interpretation of the documentation) 2) Statistics asymmetric, with conect: 36791 asymmetric, with conect, with missing atoms: 40 asymmetric, with conect, > 1 model: 2336 asymmetric, with conect, > 1 model, with missing_atoms: 38 biological, with conect: 59933 biological, with conect, with missing atoms: 3624 biological, with conect, > 1 model: 8126 biological, with conect, > 1 model, with missing_atoms: 885 The full results are (temporarily) available either as compressed CSV format file (692 kb) or as compressed MySQL dump (711 kb): http://www.fli-leibniz.de/~rhuehne/jmol/analyze_conect-2007_11_25-csv.zip http://www.fli-leibniz.de/~rhuehne/jmol/analyze_conect-2007_11_25-mysql.zip The colums are defined as follows: 1) id: PDB ID 2) unit_type: asymmetric/biological 3) unit_number: biological unit number or zero for asymmetric unit 4) maximum_model_number: largest model number found, -1 if no "MODEL" line found 4) models_with_conect_count: number of "CONECT" record sets 6) connected_atom_count: number of atoms referred to in "CONECT" records (missing atoms were not counted because they couldn't be classified) 7) connected_hetatom_count: number of hetatoms referred to in "CONECT" records (missing atoms were not counted because they couldn't be classified) 8) missing_atom_count: number of atoms/hetatoms referred to in "CONECT" records that were not found in at least 1 model 9) missing_atoms: complete list of missing atoms in Jmol-like manner (atom number/model_number) Since Jmol currently applies the "CONECT" record only to the last model before the "CONECT" record it doesn't comply with the PDB format specification. I think this should be changed. Regards, Rolf ------------------------------------------------------------------------- SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
