I am actually dealing with a structure containing an unnatural ligand.
I generated the pdb file by drawing it on PRODRG server, I did a manual
pre-fit in the map using coot and I manually merged the pdf file of my
protein with the one of the ligand.
After that I did few cycles of refinement using Refmac5, with my mtz, my
merged pdb file and the cif library of the ligand as input files.
First I saw that even if Refmac "completed succesfully" it didn't modify
coordinates of the ligand, second I saw a warning about the "DRG" molecule
in the log of Refmac (WARNING: duplicated name of monomer DRG Last entry
will be used.), third in Coot I cannot use "Real Space Refine Zone" with
the ligand and when I try to import the CIF dictionary produced by PRODRG
(through the server or even the one generated through CCP4 ProDrg), it
causes Coot crash (** (coot-bin:4467): WARNING **: Widget not found:
/programs/i386-mac/ccp4/7.0/ccp4-7.0/bin/coot: line 288: 4467 Segmentation
fault: 11 $coot_bin "$@").
Clearly I am not a skilled user of all these programs, so I certainly did
a/some mistake/s, but if someone can give me tips to be able to refine my
ligand... Should I rename my DRG molecule, should I verify particular
things, should I use other ways to generate the pdb and the library of my
P.S.: I am running CCP4 and coot using SBGRID on a Mac.