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Re: [Imgcif-l] Issue with image array directions

Dear Andy,

Sorry, have now made them a+r. D'oh!

The non-squareness of the detector is clear: this is what raised the whole question in the first place! However I am not sure if (i) I have something inconsistent in the cif (ii) mosflm is reading the image wrong or (iii) adxv is reading the image wrong. The prior probability would bias towards (i) - now that the frames are readable perhaps others can comment?

We're aiming for a full and complete cif header now which should at least match what is produced by ADSC.

Thanks & best wishes,

Graeme

________________________________________
From: Andy Arvai [arvai@scripps.edu]
Sent: 08 June 2011 17:33
To: imgcif-l@iucr.org; Winter, Graeme (DLSLtd,RAL,DIA)
Cc: cn@adsc-xray.com
Subject: RE: Issue with image array directions

Hi Graeme,

I don't't have read permission on either of these files:

> http://www.ccp4.ac.uk/xia/adxv-happy-mos-not.cbf
> http://www.ccp4.ac.uk/xia/mos-happy-adxv-not.cbf

If you can confirm which is correct, I'll make sure it displays
correctly with adxv.

By the way, pilatus images are not square (2463 x 2527 pixels) and they
have displayed correctly in the past with both adxv and mosflm, however
they don't have a "normal" cbf header. Non-square cbf files written
from XDS also work with adxv, but these also have a similar non-standard
header.

Andy

>From Graeme.Winter@Diamond.ac.uk Wed Jun  8 08:17:43 2011
>From: <Graeme.Winter@Diamond.ac.uk>
>To: <imgcif-l@iucr.org>
>CC: <arvai@scripps.edu>
>Subject: RE: Issue with image array directions
>
>Dear Chris,
>
>Version: ADXV 1.9.8b, which I gather is reasonably recent.
>
>A good suggestion: I will make both permutations of images available shortly. One comment I would make though is earlier images from e.g. the ADSC were square so it would be impossible to spot when the parameters were back to front. I am also not sure who's wrong, adxv or Mosflm, which is why I ask here.
>
>http://www.ccp4.ac.uk/xia/adxv-happy-mos-not.cbf
>http://www.ccp4.ac.uk/xia/mos-happy-adxv-not.cbf
>
>These are a pair of frames with the only (real) difference being the ARRAY1 size parameters - ADXV gets one right, mosflm the other.
>
>Best wishes,
>
>Graeme
>
>
>-----Original Message-----
>From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On Behalf Of Chris Nielsen
>Sent: 08 June 2011 16:08
>To: The Crystallographic Binary File and its imgCIF application to image data
>Cc: arvai@scripps.edu
>Subject: Re: [Imgcif-l] Issue with image array directions
>
>      Hi Graeme,
>
>      Images displayed correctly with adxv in the past (images from, say, SSRL 12-2).  Are
>you using the latest adxv?
>
>      I'd also suggest giving Andy Arvai a web url to download the images in question and test
>them himself.
>
>      Best,
>
>      Chris
>
>________________________________________
>From: imgcif-l-bounces@iucr.org [imgcif-l-bounces@iucr.org] on behalf of Graeme.Winter@Diamond.ac.uk [Graeme.Winter@Diamond.ac.uk]
>Sent: Wednesday, June 08, 2011 7:56 AM
>To: imgcif-l@iucr.org
>Subject: Re: [Imgcif-l] Issue with image array directions
>
>Aha, no attachments:
>
>http://www.ccp4.ac.uk/xia/A-adxv.png
>http://www.ccp4.ac.uk/xia/A-mosflm.png
>
>(images are deliberately blank: we are in shutdown)
>
>Best wishes,
>
>Graeme
>
>-----Original Message-----
>From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On Behalf Of Graeme.Winter@diamond.ac.uk
>Sent: 08 June 2011 15:55
>To: imgcif-l@iucr.org
>Subject: [Imgcif-l] Issue with image array directions
>
>Hi Folks,
>
>This morning while working on full-cbfifying Pilatus images I found an interesting (or at least noteworthy) feature: mosflm and adxv disagree about the correct definitions for the fast / slow image sizes. If I load an image with header containing this:
>
>loop_
>_array_structure_list.array_id
>_array_structure_list.index
>_array_structure_list.dimension
>_array_structure_list.precedence
>_array_structure_list.direction
>_array_structure_list.axis_set_id
>ARRAY1 1 2527 1 increasing ELEMENT_X
>ARRAY1 2 2463 2 increasing ELEMENT_Y
>
>I get the images attached - mosflm has it about right and adxv has it mangled. Switching these (which I think is correct: at least it corresponds to the subsequent MIME header) as follows adxv is happy but mosflm makes a mess.
>
>loop_
>_array_structure_list.array_id
>_array_structure_list.index
>_array_structure_list.dimension
>_array_structure_list.precedence
>_array_structure_list.direction
>_array_structure_list.axis_set_id
>ARRAY1 1 2463 1 increasing ELEMENT_X
>ARRAY1 2 2527 2 increasing ELEMENT_Y
>
>The thing is that (as I understand it) both are using cbflib so what's happening? I guess an issue is that the only "real" cbf images to date have been square.
>
>Any suggestions?
>
>Thanks in advance & best wishes,
>
>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
 



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