[Chimera-users] write out adjusted EM map?

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 6 09:59:19 PDT 2006

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:

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:

I hope this helps,

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
> ---------------------------
> Jesse Brown
> Research Technician
> TSRI, Dept. of Cell Biology
> 858.784.8598
> jbrown at scripps.edu
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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