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

Bernard Heymann bernard_heymann at nih.gov
Fri Sep 7 12:09:28 PDT 2007

Hi Tom

I believe the MRC specification was changed recently from unsigned  
8bit to signed 8bit to make it more compatible with the CCP4 map  
format. However, this leaves a lot of programs out there that still  
follows the unsigned convention (including IMOD), as well as a lot of  
old image files with this convention. I would suggest having a more  
explicit handling of this issue in Chimera when reading an MRC file.

On Sep 7, 2007, at 2:33 PM, Tom Goddard wrote:

>> 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
> standard.
>  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).
>    Tom
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Bernard Heymann, Research Fellow
Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH
Bethesda MD 20892-8025
Tel. 301-451-8241, Fax. 301-480-7629

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