Thank you all for the input. I think my problem got solved. The structure was determined by cryo-EM at 3.2 A. I used phenix.real_space_refine to refine the structure using the model with no hydrogen. the statistic report directly from phenix was pretty good but not from pdb validation server (especially the clashscore changes a lot). As John and Sharan mentioned here that the PDB server calculates the clashscore with the hydrogen added and that makes the difference.
What I did is adding the hydrogen first and followed by one run of phenix refinement. Finally, the problem got solved, the clashscore was dropped to 2 reported from both the phenix and PDB server. I do consider the alternative conformation and symmetry. While I think adding the hydrogen is the key to my case. Thank you again for your kindly suggestion. I wish my case may serve the people who have the similar problem in the future. Xiaodi ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of John Berrisford <j...@ebi.ac.uk> Sent: Wednesday, January 16, 2019 12:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] clashscore question Dear Xiaodi The wwPDB validation service does indeed add hydrogens using Reduce before calculating clashes. For more details of what processes are run when generating the wwPDB validation report see the on-line help https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#close_contacts If you would like us to look into this in more detail please can you email us directly on validat...@mail.wwpdb.org<mailto:validat...@mail.wwpdb.org> with details of your validation session. This email address is also listed on the wwPDB validation help page https://www.wwpdb.org/validation/validation-reports Regards John From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Sharan Karade Sent: 16 January 2019 04:28 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] clashscore question Dear Yu, I think pdb validation server add hydrogen to the structure and then calculate the clashscore. The other methods you mentioned calculate clashscore without adding hydrogen to the structure. Regards Sharan On Tue, Jan 15, 2019, 11:23 PM Xiaodi Yu <uppsala....@hotmail.com<mailto:uppsala....@hotmail.com> wrote: Hi All: I have a pdb file and the clashscores reported from both phenix and MolProbity were around 5, while the clashscore from the pdb validation server is 17. I wonder what may cause the difference? Any suggestion is appreciated. Thank you. Xiaodi ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
