"sketcher" - huh... OK, that would not be my first choice, but it should
work.
> Following this I have refined it using REFMAC5 and
> when output file was opened into coot I don't see the bond of C=O (O4)
> of the ligand but coordinate for this atom is present in the input pdb
> file.
This is two steps in one... My a priori prejudice is that Refmac doesn't
lose atoms. You need to assure me that this is that case before we move
on to talk about Coot. So, for example, grep the atom name and comp_id
in the input file, show that that is successful and the same grep on the
output file is not. Or grep the comp_id for the input and output files,
pass that through wc and show that the results are different.
> When this did not work I thought generating the cif file file from
> PHENIX (elbow) using the PDB file fitted in coot.
Urgh. This is a last resort method.
Rather than try to recover from where you are, I'd advise starting from
scratch and doing it the easy way. Using you starting mol file (or
whatever) use Acedrg or Grade or Phenix elbow to generate a dictionary.
Fit the ligand using Coot or your favourite ligand fitting program.
On 10/06/2016 18:39, jeorgemarley thomas wrote:
> The cif file I have used for the fitting the ligand in coot was
> generated from "sketcher" through which the local refinement was done.
> Then I used this ligand pdb to incorporate into the main protein
> structure coordinate. Following this I have refined it using REFMAC5 and
> when output file was opened into coot I don't see the bond of C=O (O4)
> of the ligand but coordinatefor this atom is present in the input pdb
> file. When this did not work I thought generating the cif file file from
> PHENIX (elbow) using the PDB file fitted in coot. Then refined with
> REFMAC but this also has the same problem, I went through the log file
> there it shows the atom O4 is missing. Then I tried PHENIX for the
> refinement, and I don't see any bond breakage over there. Of course I
> did not go through reverse order. Please suggest what is the possible
> reason for this.
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