[phenixbb] Waters in FEM

[Pavel Afonine]

Could you please try latest Phenix from nightly builds or send me files 
off-list and I will try right now?
Pavel

On 10/22/14 3:22 PM, Murpholino Peligro wrote:
> 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 
> <mailto: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
>>     <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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