Rolf Huehne wrote: >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. > > > sure -- that's fixed now. Have you tried 11.3.50?
>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. > > > I do, too. Sounds like the connection should be applied to all models present. And missing atoms should be ignored. I will implement that. Bob >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 >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
