Hi Mohamed, MEM = maximum entropy method. This was a quick attempt to implement MEM-based map modification, as described here (admittedly quite sketchy): http://phenix-online.org/presentations/mem.pdf All in all, this works great with very high resolution data (better than 1A), compare usual 2mFo-DFc (blue) vs MEM (red) maps (this is a 0.6A resolution data set): https://www.dropbox.com/sh/0js402ab87779e0/AAAOpEMN5iDa2Z5qniKpatARa?dl=0 To make it work similarly well at lower resolutions more work is required; so in this sense this is an unfinished project. FEM = Feature Enhanced Map: Acta Cryst. (2015). D71, 646-666. FEM: feature-enhanced map P. V. Afonine, N. W. Moriarty, M. Mustyakimov, O. V. Sobolev, T. C. Terwilliger, D. Turk, A. Urzhumtsev and P. D. Adams http://phenix-online.org/presentations/fem_06MAY2014.pdf Pavel On 3/31/15 5:19 PM, mohamed noor wrote:
Dear developers
What is the difference between MEM and FEM maps? I read the documentation and my understanding is both are supposed to create beautiful maps :)
My problem is I have a structure at 1.9 A (a different protein than the one referred to in my previous question), the Rfactor is around 20/22 %, Rms bonds is 0.03 and Rms angles is 1.845. If the bonds/angles get lower, the Rfactor jumps up (same problem as the other structure).
Looking in Coot, there are positive and negative density and missing density for the side chains of residues with high B factor. For some reason, phenix.refine keeps on adding water at strange places even at regions that I suspect to be just noise. For this reason, I want to see if the noise is really noise. A second reason is I have density that seem to be too big for a water molecule but waters were placed anyway, so I want to know if these are real positive density.
The dataset was obtained from only 50 degrees, SG is P 61 2 2. Including more images brought up the Rmerge to 30-40% and Rfactor being stuck at 30 %. For some reason, I don't find the X-ray statistics from the phenix.model_vs_data logfile but in essence, I have:
28-1.9: 82 % 6 A - infinity: 95 % in the shells (2.25-2.14, 2.14-2.04, 2.04-1.97, 1.97-1.9) my completeness is around 85-62 % and CCwork is at least 70 % and CC1/2 of the dataset is 60 % at the highest resolution shell.
Thanks.
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