Forgot the picture! Here is it!
________________________________________
From: Paul Emsley [[log in to unmask]]
Sent: Sunday, September 14, 2014 6:16 PM
To: Wang, Bing
Cc: [log in to unmask]
Subject: Re: [ccp4bb] ligand mismathces in pdb deposit
On 12/09/14 23:28, Wang, Bing wrote:
> Hi guys,
Hello.
>
> A quick question about pdb deposition! My protein has a common ligand
> 'heme' which mismatches with the ligand in pdb CCD (/Chemical
> Component Dictionary/).
What makes you think so?
> However i didn't find any differences in it. Is that because of the
> positions of double bonds or hydrogen atoms,
unlikely.
> 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.
It is not clear to me what test you are performing. I do note that the
SMILES for HEM in the CCD doesn't contain Fe - that might be related.
HTH,
Paul.
|