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 use? The latter can affect the score a bit although I've never seen this much of a difference.
HTH, Robbie On 16 Jan 2019 05:22, Xiaodi Yu <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
