saving transformed map
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 ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Thank you!!!! It works very well! Best Ariane On Apr 25, 2012, at 1:16 PM, Elaine Meng wrote:
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 ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
participants (2)
-
Ariane Briegel -
Elaine Meng