[phenixbb] Waters in FEM

Murpholino Peligro murpholinox at gmail.com
Wed Oct 22 15:22:28 PDT 2014


I also can see something like that...
https://www.dropbox.com/s/lfd2sz44b4yzu5c/water19.png?dl=0

purple is FEM and blue is normal map.




2014-09-09 1:36 GMT-05:00 Pavel Afonine <pafonine at lbl.gov>:

>  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?
>
> Thanks!
> Pavel
>
>
> 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
>
>
>   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
> phone: 573-884-1280
> fax: 573-882-2754
> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
>
>
>
>
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