[Chimera-users] Save a transformed density map

Thomas Goddard goddard at cgl.ucsf.edu
Thu Jan 24 16:56:29 PST 2008

Hi Keren,

   Chimera has a resampling capability for extracting regions of a map 
that aren't aligned with the axes.  It doesn't work well in the case you 
want.  So I've made a Chimera command that will do what you want.  If 
your the map you wish to save in the new orientation has id number 0 
(listed next to the name of the map in volume dialog), and the map you 
fit into has id 1 you would use the command:

	vop #0 resample onGrid #1

The vop stands for "volume operation".  (Use menu Favorites / Command 
Line to type commands.)  This will create the new map which will appear 
in the volume dialog and can be saved with the volume dialog File / Save 
map as... (or using a command like "volume #2 save /tmp/newmap.mrc").

   The vop command with the resample operation will be in tonight's 
builds of Chimera (assuming they succeed).



Keren Lasker wrote:
> hey Tom,
> I need to save the transformed map for other calculations. Is there a 
> resampling option in chimera? if not I guess that I can use the output 
> transformation matrix generated by fit map2map - right?
> thanks,
> Keren.
> On Jan 24, 2008, at 3:27 PM, Thomas Goddard wrote:
>> Hi Keren,
>>  You can save the Chimera session to preserve the orientation of one 
>> map fit into another.
>>  If you want to write a new map so that when it is loaded in Chimera 
>> and other software it will be at the correct place in the map it was 
>> fit into that is harder.  The problem is that none of the map file 
>> formats provide for a positioning transformation in the header.  So it 
>> would be necessary to resample the map that you fit on the grid of the 
>> map you fit into.  Resampling interpolates data values and can degrade 
>> map quality.  Do you want to do that?
>>     Tom

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