Hi Jesse, Our volume data expert is out on vacation for the next two weeks and may issue a better reply or new code when he returns. I can't offer suggestions on other software or speak to the future priorities, but I can describe the current status:

Chimera only allows you to save the untransformed EM data (with File... Save As in Volume Viewer), although it can be a subregion or zone of the original data. The possible formats for saving are NetCDF and MRC (MRC 2000; older MRC-reading programs or programs expecting CCP4 format will read such files successfully but may not align the data correctly with other data sets).

Chimera includes several accessory programs for processing volume data, but I don't know if rotation/translation could be accomplished with a function applied pointwise, for example. These programs write out NetCDF format only. Descriptions of the accessory programs: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ volumeviewer.html#processing

Actually, you might consider saving the PDB files matched to the EM map rather than vice versa. Even after you have rotated/translated everything in Chimera, you can save the PDB structures relative to the *untransformed* EM data, as described in: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html

I hope this helps, Elaine

On Jul 5, 2006, at 6:51 PM, jbrown wrote:

Hi,

I've recently used Chimera to manually fit several PDB subunits into my EM map. I am trying to figure out a way to write out the EM map in CCP4 format with the adjusted rotation/translations that I performed during my fit. Is there anyway to do this in Chimera (or are there any other programs you would suggest)? Also, any plans to include a means for writing out EM maps from Chimera in future versions?

Thanks a lot, Jesse

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Jesse Brown Research Technician TSRI, Dept. of Cell Biology 858.784.8598 jbrown@scripps.edu

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----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html