[Chimera-users] saving maps generated with molmap - origin?

Tom Goddard goddard at cgl.ucsf.edu
Tue Aug 19 10:23:23 PDT 2008

Hi Greg,

  The trouble is you are writing out the map in BRIX format which I 
believe only allows integer grid index values for the origin of the 
map.  The molmap command creates a map whose origin is not at an 
integral grid index.

  I could be wrong about the BRIX format, it may allow floating point 
origin values, but the documentation for BRIX does not say and gives 
example code for writing the file which uses integer format.  I guess 
the next step is to try writing a floating point origin in to the text 
BRIX header and open it in O and see what happens (error, misaligned, or 
correctly aligned).

  To avoid this problem you can write your map out in MRC format.


Grigore Pintilie wrote:
> Hello,
> I'm wondering why when I generate a density map from a pdb structure
> (using the molmap command) and then save it, once I reopen it it seems
> to have shifted with respect to the structure. I'm noticing that
> before saving it, the generated map has a certain origin (shown in the
> Coordinates pane in the Volume Viewer), and then when I reopen it the
> origin appears as 0 0 0. If I copy the origin shown initially and then
> paste it into the origin of the opened file, this shifts the map to
> the correct position, but why isn't the right origin saved with the
> file?
> I'm using alpha version 1 build 2509 2008/05/01, platform win32
> Many thanks,
> Greg
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