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 [email protected] <mailto:[email protected]> 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 <[email protected]> On Behalf Of Sharan Karade Sent: 16 January 2019 04:28 To: [email protected] 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 <[email protected] <mailto:[email protected]> 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 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
