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

[Tom Goddard]

Hi Helge,

The underlying reason that it is hard or impossible to show your aligned maps in Coot without resampling is because the file formats like CCP4 and MRC and others for the maps don't include any header information about how the map should be rotated in the physical coordinate space.  They do have some information about how it is shifted, but for instance with CCP4 format the shift can only be an integer number of grid points.  So to show one map fit into another the software needs to be able to input the position information that it won't get from the file itself.  I don't know if Coot can do that and you would need to ask in a Coot forum to figure that out.

	Tom

> On Jan 26, 2022, at 8:25 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Helge,
> As far as I know, you would have to resample in order to save one map relative to another and actually have the orientation saved in the file, as explained here:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#afterfitting>
> 
> Theoretically you could just save the rotation/translation information instead, but then every time you open the map file, you have to apply that rotation/translation in an additional step.  See how to save/apply ChimeraX positions files:
> <https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html>
> 
> See also "view matrix" and "measure rotation"
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix>
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>
> 
> The other alternative is to save the session, which will retain the relative orientations.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jan 26, 2022, at 3:01 AM, Helge Paternoga via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hi,
>> 
>> I would like to know if it is possible to save a .mrc map relative to another one. Basically, I would like to superpose two volumes and compare them outside of ChimeraX (i. e. using Coot) without resampling in ChimeraX, as it is my understanding that resampling changes the volume in question. I noticed that "fitmap" outputs the rotation etc. in the log, but I do not know if and how I can apply this to a map.
>> 
>> Many thanks in advance,
>> 
>> Helge
> 
> 
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