[Chimera-users] output hdf5

Tom Goddard goddard at sonic.net
Tue Oct 13 14:35:57 PDT 2015

Hi Gijs,

  Chimera can probably directly read your HDF density map if you have it read it using Chimera map format.  If you use File / Open… in Chimera and choose File Type: All (ask type) and specify Chimera map.  It won’t get the grid spacing but it will look in the HDF5 file for any 3d arrays and show them.  The format of this Chimera specific density map is briefly described at the top of the Python code


which is included in your Chimera distribution in


or on Mac


If you wanted other software to read your files you might instead use the format used by EMDB, namely CCP4 or MRC:

	http://www.emdatabank.org/mapformat.html <http://www.emdatabank.org/mapformat.html>

For an example of Python code that reads and writes that format you can look in Chimera




> On Oct 12, 2015, at 7:26 PM, gijs wrote:
> Dear Sir/Madam.
> First of all I want to complement the chimera team for writing a fantastic package for view macromolecular complexes. 
> I am a researcher from the coherent X-ray diffraction community and we are also producing 3D models using our software [1]. However, we write data in a hdf5 format. Would you be interested to incorporate our file system into your package, or, and I think this is for now the better solution, could you provide a way I can write my hdf5 file to a chimera readable format and visa versa? For instance, I am trying to open a .map file from the EM databank, but do not know to exactly how to convert it. Are there tools? What file tree in hdf5 do I need?
> With kind regards,
> Gijs van der Schot
> [1]  http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.098102 <http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.114.098102>
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