[chimerax-users] Aligning volumes without resampling - Saving a map relative to another

[Tom Goddard]

Hi Helge,

  As you can see in the MRC 2000 specification which ChimeraX tries to follow

	https://www.ccpem.ac.uk/mrc_format/mrc2000.php <https://www.ccpem.ac.uk/mrc_format/mrc2000.php>

The "skew matrix" is in the space labeled "EXTRA" in the header and the comments below say "CCP4 uses words 25-37 for defining skew planes."  CCP4 is a (slightly) different format than MRC.  ChimeraX writes MRC not CCP4 and so does not write those skew matrix fields.  ChimeraX reads CCP4 format maps but still ignores the skew matrix fields.  In about 20 years of Chimera and ChimeraX reading CCP4 files no one has ever reported an alignment bug where skew matrix was used.  So it has been my hunch that no one uses that.  And so ChimeraX currently does not support it.

	Tom

> On Jan 28, 2022, at 7:01 AM, Helge Paternoga via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> I have asked in the Coot forum and it was mentioned that there is a feature called "skew transformation" that is defined in the MRC/CCP4 2000 specification.
> 
> See here for the comment: https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2201&L=COOT&D=0&O=D&P=16005
> 
> It is mentioned that this is already used by Pymol, so I was wondering if this would be useful also for ChimeraX?
> 
> Best,
> 
> Helge
> 
> 
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