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
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
participants (2)
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Keren Lasker -
Thomas Goddard