Hi
As far as I know Paul and Eugene are working very hard to make this
option painlessly available to users. With the current versions of
refmac and coot I would check carefully at every stage. In coot I
would look at the distance berween atoms supposed to be linked (even
if they are not shown as bonds it does not mean that they are not
bonded)
After coot I would check in the pdb file that link record is present.
If I am wrong, Paul will correct me.
regards
Garib
On 17 Jul 2010, at 00:18, Subhangi Ghosh wrote:
Hi All,
I used JLigand to form a covalent bond between ligand, Benzoate and
residue Ser and followed the tutorial in the JLigand website and
refined it. How shall I know that a covalent bond is existing now?
It does not show in coot as a bond. Also although i had inserted the
line with Link befor ethe Cryst1 in my i/p pdb file, the o/p file
does not have any line specifying the link. The Benzoate also shows
up as a different chain (like if I were to add it without creating a
bond). Does that mean the for some reason the bond did not form?
Thank you,
Subhangi
