Well, that was not a simple fix. Jmol 11.3.62 has this fixed, Rolf. 1) All PDB file structures are copied into each model. 2) Using "calculate structure" you can turn any selected-model structures into Jmol-calculated ones. 3) Trajectories incorporate PDB file-derived structures, and depending upon which trajectory you select, you can do "calculate structure" based on that geometry.
I also note that calculate hbonds is broken in 11.3.59-11.3.61. But that's fixed in 11.3.62 as well. I'm sure there are more nuances with this trajectory business that I need to work out. Bob Rolf Huehne wrote: > 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 > > -- 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: 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
