I have now sorted things out and established that: 1. 'restrict (0)' supported in Jmol 10 has to be replaced by 'restrict none' I don't mind that. I knew it was a silly hack when I couldn't get things to work for some other reason and should have changed it. 2. The edited pdb files with Hydrogens added screw up the parsing of certain atoms in Jmol 11 and give them a clubfoot appearance. Why Jmol 10 tolerated this I'm not sure. Anyway, one can hardly blame Jmol. I've had so much grief processing Richardson 500 files. The 228 in my database are from 300 - 70 thrown away. I can see my having to scan all 228 files by eye for this sort of format problem. 3. I think there is a bug in jmolSetCheckboxGroup().
I have mounted one of my tests that illustrates this at: <http://doolittle.ibls.gla.ac.uk/leader/jmoltest/> As regards the jmol.js bug, check All Motifs and then uncheck any of the ones below. All remains checked. Other aspects of it are ok. I apologize for not testing this before, as I asked for this sort of thing to be incorporated. As regards the bad display, select single motif display and then Catmat: 48,48,50 . Glu 50 is screwed up. If you want to see the Jmol10 version, go to: <http://doolittle.ibls.gla.ac.uk/motif> choose Ligand Proximity and 1MFM and 3D Display to see the corresponding Jmol10 version done on the fly from the database. David -- _______________________________________________________________ David P.Leader, Biochemistry and Molecular Biology Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 41 330-5905 http://doolittle.ibls.gla.ac.uk/leader _______________________________________________________________ ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
