[Imgcif-l] Direct beam vector / direction

[Graeme.Winter at Diamond.ac.uk]

Dear Herbert,

Thanks for the confirmation - the approach I have taken is therefore to fetch it out as follows (using pycbf)

    # find the direct beam vector - takes a few steps
    cbf_handle.find_category('axis')

    # find record with equipment = source
    cbf_handle.find_column('equipment')
    cbf_handle.find_row('source')

    # then get the vector and offset from this
    
    beam_direction = []
    
    for j in range(3):
        cbf_handle.find_column('vector[%d]' % (j + 1))
        beam_direction.append(cbf_handle.get_doublevalue())

Is this the most efficient way to extract the values? It would make sense that there should be a way to extract the whole vector in one go but I could not see it (certainly not in the pycbf api)

I am slightly worried about efficiency as the first step in xia2 processing is to inspect every single image header, which for 1000 + (or even 10k) image headers could be considerable... not that these parameters will change from one frame to the next.

Many thanks,

Graeme

-----Original Message-----
From: imgcif-l-bounces at iucr.org [mailto:imgcif-l-bounces at iucr.org] On Behalf Of Herbert J. Bernstein
Sent: 23 June 2011 12:09
To: The Crystallographic Binary File and its imgCIF application to image data
Subject: Re: [Imgcif-l] Direct beam vector / direction

Yes -- that all sounds right. -- Herbert

=====================================================
  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  yaya at dowling.edu
=====================================================

On Thu, 23 Jun 2011, Graeme.Winter at Diamond.ac.uk wrote:

> Hi Folks,
>
> So, I am looking very closely into the cif side of imgCIF now and have started to wonder about how / where we record the direct beam vector. Specifically:
>
> - the rotation axis is canonically 1, 0, 0
> - the component of the vector from sample to source PERPENDICULAR to the primary rotation axis is 0, 0, 1
>
> In the example CIF headers in the big book (Tables G) there is a
>
> SOURCE general source . 0 0 1 . . .
>
> record which I assume would be the place (small values for 0 0 assumed, near unity for 1 when we add in "real" values) however there does not appear to be a mechanism in cbflib to extract this easily, in the same way that there is for the rotation axes and detector orientation.
>
> Before I start to code up a mechanism to fetch this out I thought I should check my assumptions first!
>
> Is this right?
>
> Many thanks in advance,
>
> Graeme
>
> Dr. Graeme Winter
> Senior Software Scientist
> Diamond Light Source
>
> +44 1235 778091 (work)
> +44 7786 662784 (work mobile)
>
>
>
>
>
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This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom