[Chimera-users] EM density map rescaling issue???

Christian Geiss geiss at biophysik.org
Tue May 13 02:06:38 PDT 2014

Dear Chimera User list,

I have a fundamental problem when loading pdb structures and EM density 
maps as *.em. The scale doesn't fit at all, with other words my pdb 
is tremendously bigger than the EM structure. One work-around is to 
resample the EM structure from current 64 px boxsize with 8.6 A 
pixelsize to 1 A pixelsize, giving
~ a 500 pixel volume, but then the volume gets quite big und my chimera 
gets really slow in handling those structures (pdb and big EM map at 
once)...is there any other way to solve this issue like scaling the EM 
structure on the fly in not such a memory consuming way...I also wonder 
if there is any information about the pixelsize in the EM header, 
because then the scaling should be done usually automatically???

Thanks in advance,


P.S. I couldn't find anything related to this in the chimera archive...
*Christian Geiss, M.sc.*
Universitaet Frankfurt BMLS
Frangakis Group
Max-von-Laue-Strasse 15
D - 60438 Frankfurt am Main
Phone: +49-(0)69-79842597
Fax: +49-(0)69-79846467
geiss at biophysik.org
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