Re: [phenixbb] Ensemble refinement

If I understand correctly, since ensemble refinement is a dynamics-based method your starting structure needs to be effectively "perfect" (i.e. a true representation of one of the conformations that makes up the real-world ensemble). Any error in your assignment that's separated from the true structure by a large enough energy barrier will throw it right out. With that in mind, I wouldn't throw out the ensemble refinement results immediately. Why not have a closer look and see what's moved substantially? There may be some clues in there for you. Cheers, Tristan Tristan Croll Lecturer Faculty of Health School of Biomedical Sciences Institute of Health and Biomedical Engineering Queensland University of Technology 60 Musk Ave Kelvin Grove QLD 4059 Australia +61 7 3138 6443 This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.

On 2 Apr 2015, at 8:28 pm, mohamed noor wrote:

Using the FEM map, I managed to remove more bad waters and add instead ions from the crystallization mix.

I tried phenix.ensemble_refinement but the Rfactor increased by 2 % (originally 19/22 % from phenix.refine).

Before it crashes at the validation point all the time, it prints out the validation summary with 0.53-3.48 % and 1.87-7.22 % Ramachandran outlier (from 0.3 %, supported by density) and a Molprobity score of 1.57-1.92 and 1.82-2.14 depending on pTLS used (original single model score was 2.08). The clashscore in both settings (pTLS=0.6 and 1) are 0.

Do I still go by the Rfactor and decide to not use ensemble refinement at all?

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