[Chimera-users] align different scale models

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jan 29 11:37:40 PST 2007

Hi Pu,

   The PDB file uses units of Angstroms.  To specify the spacing between 
grid planes of your EM map, open it in Chimera, then use menu entry 
Features / Origin and Scale from the volume dialog.  The "voxel size" 
values listed indicate the size of one grid cell in the density map 
which is equivalent to the grid spacing.  You can change the values and 
press Return (or Enter) key and the map will be shown at the new scale. 
  Enter the values in Angstroms.  (Chimera does not know what units you 
are using but all data sets must use the same units if you want them to 
be displayed at the correct relative scales.)  The map file is not 
modified.  To save the new scale you either can save a Chimera session 
(File / Save session as... on the main Chimera window) or save a new 
copy of the map (File / Save map as... on the volume dialog).


P Qian wrote:
> Hi Tom,
> I have question to ask you about alignment of PDB model and EM density map. 
> When I open both EM density map and its corresponding PDB model, I found they
> have different size. I think that is due to different scale they are using. My
> question is: Is it possible for me to re-scale them individually so that they
> can match each other. I cannot do it at the momemt because zoom function will
> affect all data loaded, not only active data but also unactive one. I'm trying
> to produce a EM density map which has same scale with PDB model to solve it,
> but if Chimera could do it as well, it will be helpful. Thanks
> Best regards
> P. Qian
> Dr. Pu Qian
> Physics Department 
> The University of Sheffield
> Hicks Building
> Hounsfield Road, S3 7RH
> UK  

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