I was using X-PLOR at the time. I later switched to a PRESidue patch. I
was not sure how many atoms must be added to a residue before a modified
amino acid becomes a linked amino acid. The PDB seems a bit adverse to
non-standard links. For example, why is NADP not two residues with a
LINK? There ar
What refinement program are you using? I assume cns.
Ihe idea with the non-standard residue works
very good, but the usual way is to PATCH the covalently
linked molecule to its respective covalently bound atom
in cns or xplor.
So, you do not need to alter your pdb-file.
Define a PRESI entry in topo
You need a LINK record in the PDB and a dictionary to describe the link.
If you run the job from the GUI with Review Restraints, the program
should write out a suitable dictionary to describe the link. Check the
distances etc to see if you agree with them. You then use the extended
pdb and tha
In general, it requires a LINK record to add the required bond. I don't
know how to set up refinement parameters. I had a similar case once (see
1ECC), and created a big non-standard residue containing both the amino
acid and ligand as one residue. (But, that was done in X-PLOR.) If
setting up link
Hall Gareth wrote:
Dear ccp4bb users,
I am currently refining a crystal structure of a protein with a
drug molecule in the active site. The drug molecule is seen, as
expected, to covalently bind to the active site. Therefore, can anyone
tell me what I need to do to alter the pdb file so as
Dear ccp4bb users,
I am currently refining a crystal structure of a protein with a drug molecule in the active site. The drug molecule is seen, as expected, to covalently bind to the active site. Therefore, can anyone tell me what I need to do to alter the pdb file so as to form a covalent bon
