Good old Val-Lys. I've noticed in the recent overhaul of the PDB they adopted the convention that any peptide less than three amino acids in length is now HETATOMs instead of ATOMs. This may be screwing up Coot's ability to link the dipeptide. I suggest you edit the PDB file to change these keywords and see if that helps.
On the other hand, I can't imagine what Coot could do to improve on the fantastic Val-Lys model in 8TLN. Surly that model is without flaw! ;-) Dale Tronrud Tim Gruene wrote: > Dear all, > > we would like to ask coot to fit the Val-Lys dipeptide of a thermolysin > structure. > We read in a PDB-file with the VK-fragment and run the "Other Modelling > Tools->Find Ligands" tool. > > Unfortunately coot rips the pair apart and only places the valine into the > density, the lysine is simply omitted. Is there a way to kindly as coot to not > separate the two when trying to find a suitable home for them? > > Ta, Tim > > > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A >
