On 08/10/13 00:42, Wei Shi wrote:
Hi all,
I was solving a protein-ligand complex structure and got a molecular
replacement solution with the protein as the search model
very good...
and now trying to fit the ligand to the electrondensity in coot. It
seems that the ligand needs to change conformation to fit the densitywell.
change from what? I'm not sure I understand this part.
So, I created the dictionary using PRODRG2 (the following link), and
downloaded CIF topology (general) from the results file page.
Somewhat long-winded way of doing it... but OK...
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
<http://www.ucl.ac.uk/%7Ermhasek/dictionary.html>
I actually don't know these days (I don't use the web server) :-).
FWIW, I'd use the CIF dictionary that had hydrogens- the one that is
compatible with Refmac.
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:
What did Coot say when you loaded the library?
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.
That would be the problem, I'dsay. Something inconsistent between the
model and the dictionary.
I am wondering whether any of you have any suggestions about how to
the fix this. Thank you so much!
I am not sure that you are usingthe right dictionary file.
But I must ask... why are you doing this? Why not just use Coot's
ligand builder? (it has a direct connection to cprodrg(part of CCP4)).
Regards,
Paul.
