[Chimera-users] Save a transformed density map

Keren Lasker kerenl at salilab.org
Thu Jan 24 16:59:46 PST 2008

Tom - thanks you !! :)
On Jan 24, 2008, at 4:56 PM, Thomas Goddard wrote:

> 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).
> 	http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
>  Tom
> 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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