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Re: [Imgcif-l] CBF Format

Hi

I'd like to concur with Nick. As far as Mosflm is concerned, the miniCBF 
is not a CBF. In my opinion, it should not be called "anything" CBF. 
Developers of some other integration programs have been rather less polite 
(privately) in their descriptions of the miniCBF.

My understanding is that the miniCBF was developed for the Pilatus 
detector for processing with XDS - which does not use image header 
information except for the image size and compression algorithm (and it 
gets these from the MIME part).

If you include the CIF fields that are present in images from the ADSCs at 
Diamond, you will not be going far wrong - see an example header at

 	http://www.mrc-lmb.cam.ac.uk/harry/herb.header

(this is a file I prepared for Herb a little while ago, and not linked to, 
so you need to use this URL). Note that it also includes the normal ADSC 
header information as a properly-formed CIF comment (i.e. free text 
delimited by ";" on lines on their own), but this is not parsed by Mosflm. 
MarCCD headers, being binary encoded, would probably not be usefully 
reproduced in the CBF header!

The beamline and data acquisition staff at Diamond expect all their PX 
area detectors to write CBFs in the same form with the same header 
information as proper CIF items; the image compression algorithm is up to 
the detector manufacturer, as long as it is one of those supported by 
CBFlib.

>From a personal point of view, I think it would be really nice if all CBFs 
(at least in the same field) conformed to the same format!

> Thanks for working on CBF support for the Mar CCD.  The image processing
> program LABELIT expects full CBF, not miniCBF.  The MIME area is not
> parsed.  You are correct in identifying the "non-optional" data items.
> This is as far as my expertise goes...it would be quite helpful if some
> Mar datasets written in CBF format were to be made available.  The most
> useful test cases would be those where the direct beam is offset from
> the detector center, but not at a 45- or 90-degree position angle.  Full
> datasets would be most useful.
>
> Nick Sauter
>
> Justin Anderson wrote:
>
>> Hello everyone,
>>
>> My name is Justin Anderson with Rayonix (formerly MarUSA).  I have been
>> given the task of adding CBF format support to the marccd program.  I
>> was hoping you could help me with a few questions that have arisen.  I
>> truly appreciate it.
>>
>> Now for the questions...
>>
>> 1)  Are miniCBF files meant to be read by imaging programs such as
>> marccd or are they expected to be converted to full CBF format first?
>>
>> 2)  What is the minimum set of fields that is necessary for an official
>> miniCBF and CBF file?  In the "Simple Example Header" in section 2 of
>> the Draft Format
>> (http://www.iucr.org/iucr-top/cif/cbf/cbf_definition.html) it does
>> mention at one point that "the above" data items are optional.  Does
>> that imply that the items below are required?
>>
>> 3)  Some items can exist in both the header area and the MIME area.  One
>> such example is the image size (e.g. fastest and second-fastest number
>> of pixels).  When reading a CBF file, should I expect to get that
>> information from the MIME, the CBF header area or would it be found in both?
>>
>> I appreciate any help you can give me.
>>
>>
>>
>> Justin Anderson                    Rayonix, LLC (Formerly Mar USA)
>> Software Engineer                  justin@rayonix.com
>> 1880 Oak Ave. Ste. 120             Evanston, IL, USA 60201
>> 877.627.9729                       847.869.1548
>>
>> _______________________________________________
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>>
>>
>
> -- 
> Nicholas K. Sauter, Ph.D.
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road
> Berkeley, CA 94720
>
> nksauter@lbl.gov
> Voice: 510-486-5713
> Fax: 510-486-5909
> _______________________________________________
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>

Harry
-- 
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH

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