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

Alex Shkumatov shkumatau at embl-hamburg.de
Wed Sep 22 01:29:44 PDT 2010

Hi Tom, Elaine

Thanks for your replies - very helpful!

I followed one of the links from Elaine's email:

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

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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