Dear Bing Wang,
To solve your problem, you may try to take a eme ligand directly from a
PDB that contains it, e.g. 1HRC.
You should download the PDB file and to copy and paste the ligand
coordinates in a new file and then use this new pdb file to refine your
structure.
It could be a good solution.
Danilo
Il 2014-09-13 00:28 Wang, Bing ha scritto:
Hi guys,
A quick question about pdb deposition! My protein has a common ligand
'heme' which mismatches with the ligand in pdb CCD (_Chemical
Component Dictionary_). However i didn't find any differences in it.
Is that because of the positions of double bonds or hydrogen atoms,
since my model don't have hydrogen atoms. Actually i replace the heme
with exact one from CCD and run refmac which give me a new pdb file.
Unfortunately, CCD still didn’t recognize the heme.
Solutions?
Thank you!!
Bing Wang
