Summary ------- It looks like Babel generates invalid CONECT records for bonds in .pdb files. The fields that are set aside for Hydrogen bonds and salt bridges in the CONECT record are not being respected.
I do not know if OpenBabel has the same problem. Detail ------ New functionality to support hydrogen bonds was recently added to Jmol. These bonds are rendered as dotted lines or as a dotted/segmented cylinder. I received a couple of complaints from people asking about why some of the bond cylinders were segmented. All of these examples were inorganic molecules but were in .pdb format. When I looked at the files, I saw that the CONECT records were formatted incorrectly. The pdb specification says that a CONECT record contains a 'source' atom followed by up to 4 'destination' atoms for covalent bonds. Fields after the 4 are reserved for hydrogen bonds and salt bridges. If you want to have more than 4 bonds, then you need to use an additional CONECT record. The spec is available at: http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html I do not know whether or not OpenBabel has the same issue. Miguel ------------------------------------------------------- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
