[phenixbb] Waters in FEM

Pavel Afonine pafonine at lbl.gov
Mon Sep 8 23:36:58 PDT 2014

Hi John,

thanks for feedback, this is very valuable as I'm still gaining 
experience with FEM and tuning the protocol based on it.

I can't tell what exactly happens unless I have data and model files and 
can reproduce the map you get. Would mind sharing the files off list so 
I can have a closer look?


On 9/7/14 2:38 PM, Tanner, John J. wrote:
> 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:
> http://faculty.missouri.edu/~tannerjj/FEMwaters/FEMwaters.html 
> <http://faculty.missouri.edu/%7Etannerjj/FEMwaters/FEMwaters.html>
> 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).
>> Pavel
>> 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.
>>> Thanks.
>>> 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
>>> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html 
>>> <http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html>
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