>> I have reproduced the problems with 1PPA. I am puzzled. I will >> investigate. >> > a hint may be, there is no secondary structure defined > in 1ppa if I inserted > TURN 1 T1 SER 1 SER 1 The dummy structure > into 1ppa.pdb > no 'hbonds' where shown.
This was a good hint, but I did not grasp the significance when I first read the message. The problem is that the built-in algorithm for calculating secondary structures is dependant upon hbond interactions. So, if there were any structures in the file, then the internal hbond calculations were not performed. However, if there were no secondary structures defined in the input file then the internal hbond calculations *do* get applied, causing undesired interactions. Miguel ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
