Hi all, while preparing multi-model images for all NMR entries in the PDB I noticed that Jmol 11.3.47 (and also 11.3.61) treats the models differently regarding secondary structure information:
For the first model it seems to use the information available in the secondary structure section of the PDB file header. But for the other models it calculates the secondary structure itself. You can look for example at entry '1p83' at http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1p83 If you expand all images at the top right you can see that for the first model only a short helix is displayed. This helix is defined in the 'HELIX' record of the PDB file (http://www.fli-leibniz.de/cgi-bin/idb_send-rh.pl?CODE=1p83&MODE=complete-asymmetric-NMR&MIME=HTML). For the other models a longer helix and a sheet are displayed. This behaviour was introduced somewhere between version 10.2.0 and 11.3.47, because 10.2.0 applies the secondary structure information from the PDB header to all models. Since the PDB format documentation (http://www.wwpdb.org/documentation/format23/sect5.html) doesn't indicate any possibility to provide different secondary structure information to different models I think it should be applied to all models (similar to CONECT records). Regards, Rolf ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
