[Biojava-dev] Support for .cif structure factors or electron density maps?

[Jose Duarte]

Support for electron density map calculation would be absolutely fantastic,
I'm all for it. Let me know if you need any help with that. It would
probably require a couple of external libraries (FFT for instance?),
perhaps this should be done on a new biojava module so that we keep the
additional library requirements out of the core structure module.

Jose

On Fri, Jan 29, 2016 at 3:34 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Matt,
>
> there is currently no code for this in BioJava, however it would be great
> to have! Any contributions in this directions would be more than welcome.
>
> Andreas
>
>
>
> On Fri, Jan 29, 2016 at 3:02 PM, Matt Larson <larsonmattr at gmail.com>
> wrote:
>
>> Are there any methods in BioJava's API to create electron density maps
>> from structure factors?
>>
>> The RCSB Protein Data Bank has switched from providing .mtz format to
>> using a .cif format for the structure factors.  BioJava already has mmCIF
>> parsing for _loop records that relate to the protein structure and could
>> probably easily support the new format for providing structure factors.
>>
>> Using structure factors /w generated phases from coordinates and to
>> create density maps would be a harder task.  Is there any interest in this
>> kind of functionality in BioJava?  I saw a recent discussion related
>> #224 ( Extend biojava-structure to better support energy minimization )
>> that looked like a promising area that could benefit from having real
>> electron density or methods for calculated structure factors.
>>
>> --
>> Matt Larson, PhD
>> Madison, WI  53705 U.S.A.
>>
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>>
>
>
>
>
>
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