problem in the future.
Xiaodi
From: CCP4 bulletin board on behalf of John Berrisford
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
https://www.wwpdb.org/validation/validation-reports
Regards
John
From: CCP4 bulletin board 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 an
Hi Xiaodi,
Please read the PDB validation report for the individual clashes and see if
these are symmetry or alternate related. If you have been playing around with
atomic occupancies, this also affects which atoms are taken into account for
the clashscore. Also, which hydrogen model did you us
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 Hi All:
>
> I have a pdb file and the c
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
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