Dear Wei,
It seems that coot detects some discrepancies between cif file and your
ligand. It is not uncommon that the program used to generate your ligand
pdb produces atom definitions that are not correctly read by programs
used to generate restrains, such as PRODRG. In order to overcome the
problem, you could try to use the pdb file of your ligand created by
PRODRG to fit the density that you believe related to your ligand.
I hope this information will will be of help for you.
Danilo
-------- Original Message --------
Subject: [ccp4bb] move ligand to fit the density in coot
Date: Mon, 7 Oct 2013 19:43:07 -0400
From: Wei Shi <[log in to unmask]>
To: [log in to unmask]
Hi all,
I was solving a protein-ligand complex structure and got a molecular
replacement solution with the protein as the search model and now
trying
to fit the ligand to the electron density in coot. It seems that the
ligand needs to change conformation to fit the density well.
So, I created the dictionary using PRODRG2 (the following link), and
downloaded CIF topology (general) from the results file page. Is this
the CIF library which I should include in order to move the ligand to
fit the density in coot?
http://www.ucl.ac.uk/~rmhasek/dictionary.html [1]
And in coot, I loaded the pdb file, mtz file and the click import CIF
dictionary to load the DRGMAC.LIB file, but when I was trying to move
the ligand, coot gave the error message as follows:
No restraints found!
No existent or minimal description of restrained residues. Are you
sure
that you read a non-minimal mmCIF dictionary for this monomer. Are you
sure the PDB reside name matches the dictionary residue name?
If not, try File -> Import CIF Dictionary
Alternatively, did you check that the atom names of the PDB file match
those of the restraints.
I am wondering whether any of you have any suggestions about how to the
fix this. Thank you so much!
Best,
Wei
Links:
------
[1] http://www.ucl.ac.uk/%7Ermhasek/dictionary.html
|