[Chimera-users] Save a transformed density map
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).
> 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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