[phenixbb] feature enhanced maps

Mads Beich-Frandsen mads.beichfrandsen at irbbarcelona.org
Thu Jul 25 03:39:26 PDT 2013

Dear Pavel,

I've been using the feature enhanced maps for a 2.1Å dataset, and it really helped for building those tricky loop-regions.
I also experience the waters to stand out clear in this type of map.

And btw., does it make any sense to calculate a FEM based on a composite omit map?

Best rgds.,

Mads Beich-Frandsen, PhD

Institute for Research in Biomedicine (IRB Barcelona)
Parc Científic de Barcelona
C/ Baldiri Reixac 10
08028 Barcelona - Spain
Tel: +34-9340-37188 | Fax: +34-9340-39960
E-mail: mads.beichfrandsen at irbbarcelona.org

On Jul 24, 2013, at 7:25 PM, Guenter Fritz <guenter.fritz at UNI-KONSTANZ.DE> wrote:

> Dear Pavel,
> I had a try today for feature enhaced maps on 3.7 and4 A resolution datasets.
> The maps look great and I feel especially at low resolution this new tool  helps a lot to interpret the maps.
> I would be very much interested to test the fem for e-densities calculated from experimental phases. Is it possible in the future to use heavy atom derived phase information instead of a model to calculate FEMs?
> Best wishes,
> Guenter
>> Hi Joseph,
>>>> Thanks Nat! I am trying out the new "Featured Enhanced Map" option.
>>>> Preliminary analysis says it really helps!
>>> Okay, that definitely isn't included in the GUI yet - I was waiting to
>>> hear from Pavel before I added it.
>>> I am sure Pavel would be interested in seeing any cases where this
>>> helps.  In general, although we obviously test new methods against
>>> existing datasets, it is always more impressive to demonstrate that
>>> they help solve new problems.
>> I'm glad it worked for you, and I'm very interested to hear any feedback or answer questions. This is still considered under development, though current implementation is stable and ready to use. There might be some changes to the algorithm in future (mostly to make it faster, so it can be routinely run after refinement, for example), but I don't think these changes will be major.
>> The only documentation at present is this set of slides:
>> http://www.phenix-online.org/presentations/fem.pdf
>> which also provides usage instructions (using command line).
>> Nat: yes, it would great to have GUI for this! Thanks!
>> Pavel
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> -- 
> PD Dr. Günter Fritz
> Fachbereich Biologie
> Universität Konstanz
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