[Chimera-users] Re: Chimera and O brix format

chimera-users at cgl.ucsf.edu chimera-users at cgl.ucsf.edu
Tue May 6 15:11:16 PDT 2003

Hi Ed,

  I wrote the SPIDER volume file reader for Chimera.  You can get it from


and unpack it

    % cd /usr/local/chimera/share
    % tar zxf spidervol.tar.gz

It includes a new VolumeData/fileformats.py that adds the SPIDER file reader
to the list of supported file formats, and a VolumeData/spider directory that
contains the Python code to read the data.

  I don't think this should be announced on the SPIDER newsgroup until we
make our next Chimera release that includes it.

  I'd like to figure out how the spacing between grid points in
physical units is handled by SPIDER.  I see a "scale" parameter in the
SPIDER file header, but the documentation says SPIDER does not use
this, and in the file you sent me it was set to zero.  Chimera likes
to know the correct scale in physical units (eg angstroms or
nanometers) so when a second model is opened they are drawn to the
same scale.  There are entry fields to hand set the scale in the
Volume Viewer dialog, but it is nicer to be able to extract this from
the file header.


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