[Chimera-users] saving transformed map

[Elaine Meng]

On Apr 25, 2012, at 9:04 AM, Ariane Briegel wrote:

> Dear Elaine,
> I have been using chimera to align several EM maps in respect to each other. 
> These maps are generated by imod (mrc format). I know I can save the transformed maps in chimera when I use the 'save session' command, but that only allows me to use the transformed maps inside chimera. I would like to save the individual transformed maps- either in mrc or CCP4 format.
> I tried to find any info about that  in the manual, then checked the old chimera list comments. I found a similar question from the year 2006 (http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-July/000864.html), but at that time your conclusion was it is not possible.
> Do you know if there is a way to do this now?
> Thank you so much for your answer,
> Ariane

Hi Ariane,
The map formats don't include transformation information, so there is no way to save EXACTLY the same data, except transformed. However, you can resample the map onto a new grid, and then save the new map.  The values at the new grid points are determined by interpolation, so there will be some (generally minor) data loss.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>

The resampling of one map onto the grid of another can be done with command "vop resample"
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>

For example:
vop #1 resample onGrid #0

To save the resampling result to a file, you could use "File... Save Map as" in the Volume Viewer dialog or the command "volume" with its  "save" option.
I hope this helps,
Elaine
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Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco