[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:

Hi John,

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.


Jack Tanner

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>
phone: 573-884-1280
fax: 573-882-2754

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