[Chimera-users] technical questions about volume viewer in chimera

Tom Goddard goddard at sonic.net
Wed Sep 22 09:23:31 PDT 2010

  Hi Alex,

   The pixel size is in the MRC file header.  It is (CELLA[0]/mx, 
CELLA[1]/my, CELLA[2]/mz).  Refer to the MRC file documentation for details.


There is a file header word MACHST used to distinguish big-endian from 
little-endian files (value 0x11 0x11 0x00 0x00 or 0x44 0x44 0x00 0x00).  
Chimera does not use that.  I think the reason is that it is not always 
set.  In fact Chimera did not set it correctly when writing MRC files 
until just yesterday.  Instead Chimera looks at the number of map 
columns (NC) and chooses the byte order that makes that value between 1 
and 65536.

   For more details of reading MRC files see the Chimera python code in 
your distribution


On Mac the share directory is Chimera.app/Contents/Resources/share.


> Hi Tom, Elaine
> Thanks for your replies - very helpful!
> I followed one of the links from Elaine's email:
> http://ami.scripps.edu/prtl_data/mrc_specification.htm
> Does this actually mean that pixel size is not provided in MRC file?
> Could you also perhaps comment on how chimera recognizes the density 
> files
> with inverted order of bytes?
> Thanks in advance
> Alex
> Quoting "Tom Goddard" <goddard at sonic.net>:
>>   Hi Alex,
>>    Chimera reads the voxel size and map grid size from the headers of
>> each of the volume file formats it reads.  Often the correct voxel size
>> is not given in the files and is set to 1.0.  If it the file has zero
>> (or negative) for the voxel size than Chimera uses of size of 1.  You
>> can change the voxel size within Chimera using the volume dialog
>> Coordinates panel.  Then you can save a new file with the volume dialog
>> File / Save Map As... menu entry.
>>      Tom
>>> Hallo
>>> Perhaps, this has been on the forum before, but I could not find the
>>> answers to
>>> my questions:
>>> 1. Some EM density maps have a header. I wonder how Chimera recognizes
>>> it and calculates map dimensions?
>>> 2. Does chimera take default voxel size from header of EM file?
>>> Thanks in advance
>>> Alex
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> ----------------------------------------------------------------------
> Alexander Shkumatov, predoc -- Biological Small Angle Scattering Group
> EMBL Hamburg Outstation c/o DESY -- Building 25A
> Notkestraße 85 -- 22603 Hamburg -- Germany
> tel:    +49 40 89902 178    fax:    +49 40 89902 149
> Email: shkumatau at embl-hamburg.de
> ----------------------------------------------------------------------

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