Thank you very one here! Got fixed from Katherine's solution! You guys are really helpful!
Bing ________________________________ From: Katherine Sippel [katherine.sip...@gmail.com] Sent: Monday, September 15, 2014 3:17 PM To: Wang, Bing Cc: ccp4bb Subject: Re: [ccp4bb] ligand mismathces in pdb deposit Hi Bing, This is the result of the new PDB deposition system being buggy. I had a similar problem with imidazole recently. This is the solution given to me by the PDB annotators. >Please choose from the instance page: >type of ligand: heterogen, >then give alternate ligand ID as IMD, (in your case HEM) >then click finish button address the issue. >It should solve the problem, if not, please let us know. Hope this helps, Katherine On Mon, Sep 15, 2014 at 3:03 PM, Wang, Bing <bingw...@ou.edu<mailto:bingw...@ou.edu>> wrote: Forgot the picture! Here is it! ________________________________________ From: Paul Emsley [pems...@mrc-lmb.cam.ac.uk<mailto:pems...@mrc-lmb.cam.ac.uk>] Sent: Sunday, September 14, 2014 6:16 PM To: Wang, Bing Cc: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> 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. -- "Nil illegitimo carborundum" - Didactylos
