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

[Christian Geiss]

Hi Tom,

that was exactly what I was looking for, but couldnt find it without a hint that something like this actually exists...

Thanks a lot!!!

All the best,
Chris

----------------ursprüngliche Nachricht----------------- 
Von: "Tom Goddard" goddard at sonic.net 
An: "Christian Geiss" geiss at biophysik.org 
Kopie: Array 
Datum: Tue, 13 May 2014 10:53:18 -0700 
----------------------------------------------------------

>
>Hi Christian,
>
> 
>
>Set the “voxel size” in the Coordinates panel of the Chimera Volume Viewer dialog 
>(menu Features / Coordinates) to 8.6. The Tomography Toolbox format *.em does include a 
>voxel size value and Chimera reads it but apparently it is not set or it is set to 1 Angstrom in 
>your map file. If you save your map as say MRC it will have the new voxel size. Or if you save a 
>Chimera session it will have the new voxel size. Chimera does not write Tomography Toolbox 
>format so it cannot rewrite that file.
>
> 
>
>Tom
>
> 
>
>
>
>On May 13, 2014, at 2:06 AM, Christian Geiss wrote:
>
>
>>
>>
>>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 structure
>>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,
>>
>>Chris
>>
>>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
>> 
>>
>>_______________________________________________
>>Chimera-users mailing list
>>Chimera-users at cgl.ucsf.edu Chimera-users at cgl.ucsf.edu 
>>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
>>
>>
-- 

Christian Geiss, M.sc.
Universitaet Frankfurt BMLS 


Frangakis Group[ -> http://www.fmls-institute.de/fileadmin/template/images/1px_trans.gif] 


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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