[Chimera-users] MRC map values -128 to 127

Tom Goddard goddard at cgl.ucsf.edu
Fri Sep 7 11:33:17 PDT 2007

> Hi,
> I have some mrc files on a 64 bit linux machine (linux version
> 2.6.9-42.0.8.ELsmp, x86_64) and the chimera on that machine displays the
> volume data fine with a range from 3 to 255 and a histogram centered
> around 120 and the 3D structure shows up very well with a threshold of
> 108. But after I transfer these data to a mac os x 10.4.10 and use the
> chimera on the mac, the data range becomes -128-127 with the histogram
> splitted into two halves close to each end of the data range. What's
> worse, I can not get a good threshold to show my 3D structure. Can you
> please tell me what is possibly wrong and how to fix this?
> Thank you very much.
> Zhiheng

Hi Zhiheng,

 The trouble with displaying your MRC files with Chimera is that the 
files contain unsigned 8-bit data values (0-255 range) and that format 
is not supported by the MRC standard.  Only signed 8-bit data values 
(-128 to 127) is supported by MRC.  So why does it work on your 64-bit 
linux Chimera and not the Mac Chimera?  I believe that is because your 
Linux Chimera is an old version of Chimera.  About one year ago 
(September 19, 2006, Chimera version 1.2290) I changed Chimera to follow 
the MRC standard and use signed 8-bit whereas earlier versions 
incorrectly assumed unsigned 8-bit values.  Your Mac version of Chimera 
is probably newer and your Linux version older.

 The MRC file header gives no indication that the values should be 
unsigned 8-bit as that value type is not supported.  But some software 
programs ignore that, use unsigned 8-bit values and set the MRC header 
field to indicate signed 8-bit.  They rely on software to ignore the MRC 

 I added a way to work around this problem in newer versions of Chimera 
(Nov 29, 2006,  version 1.2315).  You open then MRC map then use the 
keyboard shortcut "u8" to reinterpret it as unsigned 8-bit.  Then you 
will need to save the map with the volume dialog menu entry File / Save 
map as... if you want to avoid using u8 every time you open the map.  
Saving a map which is unsigned 8-bit will automatically use the signed 
16-bit MRC mode.  You probably should not overwrite your original file 
but instead make a new file.  To use this u8 shortcut you first have to 
turn on shortcuts with Chimera menu entry Tools / General Controls / 
Accelerators On.  Then you can type u8 in the main Chimera window.  It 
operates on the map currently shown in the volume dialog so you can 
switch maps and apply it to other maps as well.  You may also be 
interested in shortcut "Im" which inverts the map, mapping the range 
value v to (255-v).


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