[phenixbb] Waters in FEM
Pavel Afonine
pafonine at lbl.gov
Wed Oct 22 15:24:54 PDT 2014
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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