T0237 (1-219)

DUE 16 Aug 2004


Thu Aug 12 14:27:16 PDT 2004 Martina Koeva

Try1 is done. Unfortunately, it has not put in the disulphide bonds 
together, even though I explicitly put them for the first try. It seems
that most of the t04 files are missing and I am not clear as to the 
reason for that. 

Otherwise, I have to say that I don't think try1 looks as bad as it used
to look before. A couple of strands have paired up into sheets. I am hoping 
that there won't be a contradiction between the sheet constraints and the 
SSBond constraints. 

For try2 I have restricted the strand and helix constraints to the ones
from t2k.dssp-ehl2.constraints, as well as the sheet constraints from 
try1-opt2.sheets:

# try1-opt2.sheets
SheetConstraint I59 V60         T25 H26         hbond V60
SheetConstraint A85 F86         E62 N63         hbond A85
SheetConstraint H139 A141       L153 H151       hbond H139

I have raised the weight on known_ssbond, as well the break weight to 40. 
If the disulfide bonds to get formed on this try, I will have to reduce 
the break weight again. Finally, I reduced the sidechain weight, which 
was set high at 6. 

I have commented out the PrintTemplateAtoms line from the .under file.