[phenixbb] ligand refinement - elbow

[Christine Gee]

Hi
Its taken me a while to get around to it, but I just ran elbow to  
create a cif file etc for my inhibitor, but the bond lengths are  
quite different from what I got from the PRODRUG server, and it seems  
that the pdb file I got out of elbow has a few problems (COOT doesn't  
join up the aromatic ring for example because the carbons are now too  
far away on one part of the ring). I was wondering how the bond  
lengths are selected?  It seems it is giving the aromatic carbons a  
bond length of 1.5, when my previous file (and phenylalanine for  
example have 1.3).  Also, I still am not 100% sure how to add the  
CONNECT information to make the ligand able to covalently bind to the  
protein.
Regards
Christine