[phenixbb] Waters in FEM
pafonine at lbl.gov
Mon Sep 8 23:36:58 PDT 2014
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:
> 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
>>> 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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