[Chimera-users] Save a transformed density map
goddard at cgl.ucsf.edu
Thu Jan 24 16:56:29 PST 2008
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?
> 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?
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