[phenixbb] Waters in FEM
Tanner, John J.
TannerJJ at missouri.edu
Sun Sep 7 14:38:31 PDT 2014
Well, this is embarrassing...the assign label window was hiding behind the graphics window.
Now that I do see the FEM, I have an observation about the FEM. Although the FEM is providing an informative assessment of the protein and bound ligands, the assessment of water is a little strange. There are several water molecules that have strong 2Fo-Fc density but absolutely zero FEM density. Even if I contour the FEM down to the lowest possible value (0.09 sigma in this case), I still see no FEM density on these waters. The waters in question have good hydrogen bonding to the protein and acceptable B-factors (26-30 Ang^2). These are waters that I would normally keep in my final model. Has anyone else seen this behavior?
Some examples are posted here:
On Sep 7, 2014, at 2:51 PM, Pavel Afonine wrote:
it does not open via Auto Open MTZ.
start Coot then
File -> Open MTZ, mmCIF, fcf or phs -> the choose FEM,PHIFEM (there are two Fourier maps in this file : FEM and usual 2mFo-DFc).
On 9/7/14 11:14 AM, Tanner, John J. wrote:
Has anyone had problems reading feature enhanced map mtz files into coot? I made an FEM on a linux computer with phenix.fem, which created an mtz file:
-rw-r--r-- 1 tannerjj tanner 10760960 Sep 7 12:21 fem.mtz
As you can see, the mtz file is not empty. The fem job appeared to have ended normally, since the last line in the out file is
FEM loop: done so far: 100%Time: 3112.3967
However, when I read this mtz into coot, the map does not appear. There is no error message from coot. I tried autoinput mtz and read mtz. I'm using coot on a mac. I have not tested with coot on Linux.
John J. Tanner, PhD
Professor of Biochemistry and Director of Graduate Admissions and Recruitment
Professor of Chemistry (Joint Appointment)
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
email: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>
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