Hi,
did you check in the refmac logfile that the cif file created at the
first step was actually read ?
If it is, you will have to carefully check the cif file and you ligand
structure :
1) is the ligand structure included in the PDB at the fisrt step
complete ?? Maybe you included only a partial lignad because of weak
density... when you add other atoms, they will be missing from the cif file.
2) are all the ligand atoms present in the cif file with correct names ?
3) are the information present in the cif file correct (connectivity,
bond order, planar group, chiral center). This will not produce the
error you have, but will certainly distort the geometry...
hope this helps
laurent
Le 12/03/2012 06:21, Dipankar Manna a écrit :
Dear All,
As I am practicing new in the crystallography, I am facing some
difficulties in refining the ligand bound structure. Protein I am
working with has SG P212121, it’s a dimer. I fitted the ligand on the
density with COOT-->calculate-->Model/Fit/Refine-->Rotate/Translate
Zone. Then I merged both (protein & ligand) the pdb structure and saved
the coordinate as .pdb file. By taking this pdb when I am running
restrained refinement it was showing:
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Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr
Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089
PICT -- Plateforme Intégrée de Criblage de Toulouse
Département Biologie Structurale et Biophysique
BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE
Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994
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