[Chimera-users] save density map relative to...

Tom Goddard goddard at cgl.ucsf.edu
Tue Jul 20 18:16:08 PDT 2010

Hi Jie,

   You want to save a map that has been rotated relative to another map 
so that when you open both maps later they align.  The difficulty is 
that the common map file formats like MRC and Spider don't have any 
place in the file header to specify a rotation.

   There are two ways to work around this limitation.  One is that 
Chimera does some special trickery and puts the rotation information 
into a "label" in MRC map files so that when it later reads the file it 
can restore it in the right position.  The trouble is that no other 
software will recognize that rotated position -- only Chimera.  Another 
difficulty is that Chimera won't record the rotated position when you 
fit one map in another.  The reason for that is because Chimera saves 
the rotation of the map grid relative to the maps local coordinate 
system.  But fitting doesn't change the orientation of the grid -- 
instead it moves the local coordinate system (the map coordinate axes 
move instead of the data moving).  Each map has its own set of 
coordinate axes.  I think it would be pretty easy to add a "save 
relative to" option to the Same Map As... dialog that would take account 
of both types of rotation.  But again, the orientation would only be 
restored by Chimera.

   The second method is to resample the rotated map on the grid of the 
map you fit into and save that resampled map.  This will allow other 
software to open the maps and show the correct alignment.  The drawback 
here is that the resampled map may have degraded quality since it 
interpolated the original map (trilinear interpolation).  The Chimera 
command to do that looks like

     vop resample #3 onGrid #2

Here #3 is the id number (shown in Favorites / Model Panel or the volume 
dialog) of the rotated map that was fit into map #2.  This will make a 
new map that you can save and it will align with map #2 when opened in 
another session or with other software since they share identical grids.



> Hi Tom,
> Hope this email finds you well. This is Jie from Joachim Frank's lab.
> We met at the UCSF molecular animation workshop.
> I am writing about the "save map as" function in Chimera. Is there a
> way to save map relative to another map (like the option available in
> "save PDB")? The fitting algorithm ("fit in map" function) in Chimera
> is very good, and I sometimes use it to align two density maps.
> However, I couldn't save the density map after it was shifted. If
> there's no such option, is it possible to add it?
> Best regards,
> -Jie

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