[Imgcif-l] RE: CBFlib status
Herbert J. Bernstein yaya at bernstein-plus-sons.comMon Apr 17 09:06:57 BST 2006
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Dear Chris,
I am copying this to the imgcif list, since this might be
useful to others working with mosflm and CBF:
If you are running a version of mosflm without the following
patch,
http://arcib.dowling.edu/~bernsteh/cbfwrap.patch
you will need to use an editor (e.g. ex or sed) to apply
the following correction to any CBF produced by convert_image:
1,$s/diffrn_data_frame/diffrn_frame_data/
You will also want to make the following edit pass to
put the sample detector distance where mosflm expects it
instead of where I mistakenly put it:
1,$s/_diffrn_detector.sample_detector_distance/_diffrn_measurement.sample_detector_distance/
With just the first change, ipmosflm runs, but with some warnings.
With both changes, ipmosflm seems to just run for the adsc
images.
Once we have collected a few more comments, I will provide internal
hooks for both these changes in a patch for convert_image.
Thanks for you patience with all this.
Regards,
Herbert
At 6:26 AM -0400 4/17/06, Herbert J. Bernstein wrote:
>Dear Chris,
>
> It looks like you are using a version of ipmosflm
>that still insists on diffrn_frame_data instead
>of diffrn_data_frame. You need to do one of the
>following:
>
> 0. Apply the patch
>
> http://arcib.dowling.edu/~bernsteh/cbfwrap.patch
>
>to mosflm.
>
> 1. Edit your cbf to have an extra copy
>of the diffrn_data_frame loop as a
>diffrn_frame_data loop and to ensure that
>it contains the sample_detector_distance.
>
>If this is too much of a nuisance, I'll just add
>an option to convert image to do the mapping
>fromn diffrn_data_frame to diffrn_frame_data
>on output. All the pieces to do that are
>there, but Harry seems to be willing to
>accept the patch.
>
> Regards,
> 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 Sun, 16 Apr 2006, Chris Nielsen wrote:
>
>>
>> Hi Herbert,
>>
>> Still no joy. Downloaded the latest, ran convert_image, and I get
>> the messages below from mosflm. There needs to be a quick index lookup
>> for "Fatal Error" numbers. I don't find an easy way to find this in
>> the source.
>>
>> Getting closer!
>>
>> Regards,
>>
>> Chris
>>
>> convert_image -i mb_LP_1_001.img -o mb_LP_1_001.cbf -d adscquantum315
>> convert_image: template_name: template_adscquantum315_3072x3072.cbf
>> HEADER_BYTES = 512;
>> DIM = 2;
>> BYTE_ORDER = big_endian;
>> TYPE = unsigned_short;
>> SIZE1 = 3072;
>> SIZE2 = 3072;
>> PIXEL_SIZE = 0.102588;
>> BIN = 2x2;
>> DETECTOR_SN = 901;
>> TIME = 29.945155;
>> DISTANCE = 200.000000;
>> PHI = 85.000000;
>> OSC_START = 85.000000;
>> OSC_RANGE = 1.000000;
>> WAVELENGTH = 0.979381;
>> BEAM_CENTER_X = 157.500000;
>> BEAM_CENTER_Y = 157.500000;
>> PIXEL SIZE = 0.102588;
>> OSCILLATION RANGE = 1;
>> EXPOSURE TIME = 29.9452;
>> TWO THETA = 0;
>> BEAM CENTRE = 157.5 157.5;
>> header pixel center indices: 1535.5 1535.5
>> Element ID: ELEMENT1
>> convert_image: beam center: 1535.5 1535.5 157.524 -157.524
>> detector distance: 200
>> Pixel area, projected area: 0.0105243 , 0.00703457
>> [ccd at cnvaio2 wide]$ cd process_cbf
>> [ccd at cnvaio2 process_cbf]$ mosflm
>>
>>
>> ************ Version 6.2.5 for Image plate and CCD data 9th
>>August 2005 ***********
>> A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD,
>>CAMBRIDGE CB2 2QH, UK
>> E-mail andrew at mrc-lmb.cam.ac.uk
>> New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky
>>and Michael Rossmann
>> (1998) J. Appl. Cryst. 30, 1036-1040
>> Original auto-indexing using REFIX due to Wolfgang Kabsch
>>(Kabsch,W. (1993),
>> J.Appl.Cryst. 24,795-800.)
>> X-windows interface using xdl_view due to John Campbell
>>(Daresbury Laboratory, UK.)
> > (Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.
>>
>>
>> MOSFLM => @mosflm.inp
>> Command filename: mosflm.inp
>> MOSFLM => scanner CBF
>> warning, warning, warning. This detector option has not been fully
>>enabled yet.
>>
>> You should be prepared for unexpected results.
>> MOSFLM => gain 0.2
>> MOSFLM => synchrotron polar 0.99
>> MOSFLM => dispersion 0.0002
>> MOSFLM => divergence 0.001 0.001
>> MOSFLM => genf genfile.gen
>> MOSFLM => wavelength 0.9794
>> MOSFLM => distance 199.43
>> MOSFLM => beam 157.52 157.60
>> MOSFLM => mosaic 0.234
>> MOSFLM => directory ../
>> MOSFLM => template mb_LP_1_###.cbf
>> MOSFLM => extention cbf
>> MOSFLM => image 1
>> MOSFLM => go
>>
>> CBFlib fatal error 4000
>>
>> CBFlib fatal error 4000
>>
>> CBFlib fatal error 4
>> [ccd at cnvaio2 process_cbf]$ ls -l ../mb_LP_1_001.cbf
>> -rw-r--r-- 1 ccd games 5773811 Apr 16 22:35 ../mb_LP_1_001.cbf
>> [ccd at cnvaio2 process_cbf]$
> >
>>
>> -----Original Message-----
>> From: Herbert J. Bernstein [mailto:yaya at bernstein-plus-sons.com]
>> Sent: Sun 4/16/2006 3:54 PM
>> To: Chris Nielsen
>> Cc:
>> Subject: RE: CBFlib status
>> Dear Chris,
>>
>> The latest and greatest is now at:
>>
>> http://arcib.dowling.edu/~bernsteh/software/CBFlib_0.7.5/
>>
>> The updated manual is at:
>>
>> http://arcib.dowling.edu/~bernsteh/software/CBFlib_0.7.5/doc/CBFlib.html
>>
>> The tarball is at:
>>
>> http://arcib.dowling.edu/~bernsteh/software/CBFlib_0.7.5/CBFlib.tar.gz
>>
>> This is not final, but further changes will go into 0.7.6, so people
>> will have this as a base to work against.
>>
>> Actually, I have not yet done a complete job on the transforms.
>> I only have the code working for square arrays, and I really
>> should allow for the possibility of unequal x and y dimensions.
>>
>> I think you will find the centering in this version fairly
>> reasonable. I rounded to the nearest half pixel. Let me
>> know if you want me to put it back to the previous handling.
>>
>> I've told every on the imgCIF list about this release to get more
>> testers. Do you want to be added to the imgCIF list? We moved
>> it from BNL to the IUCr.
>>
>> Regards,
>> Herbert
>>
>>
>> At 3:05 PM -0700 4/16/06, Chris Nielsen wrote:
>> > Hi Herb,
>> >
>> > I'll give this a try. Apropos the beam center, well, you always
>> >worry about something missed when the math does not work out, so I'm
>> >with you.
>> >
>> > When I can get things to process (which I expect, now) I will
>> >be in a position to understand where we are with this format. Note
>> >well that mosflm has always displayed "normal" adsc images mirrored
>> >and rotated; that's because of its origin as a film processing
>> >package. Everyone lives with that distinction when the images are
>> >processed. Fortunately, you built in *all* necessary mirror and
>> >rotations into the conversion, so we're set. Since mosflm's
>> >view is not natural we may elect to output adsc images in the
>> >"normal" orientation and continue to view mosflm images with its
>> >mirror and rotation. Normally "detector adsc" takes care of
>> >the origins, etc., for adsc images but this can be explicitly
>> >set as well, since scanner (or detector) cbf will nor correspond
>> >to the adsc convention.
>> >
>> > I am sure this will sort out shortly.
>> >
>> > Thanks again for the hard work,
>> >
>> > Chris
>> >
>> >
>> >-----Original Message-----
>> >From: Herbert J. Bernstein [mailto:yaya at bernstein-plus-sons.com]
>> >Sent: Sat 4/15/2006 4:14 AM
>> >To: Chris Nielsen
>> >Cc:
>> >Subject: RE: CBFlib status
>> >Dear Chris,
>> >
>> > You need to say
>> >
>> > scanner CBF
>> >
>> >The entire script follows below, but I should mention that
>> >the biggest problem I am now having on finishing the
>> >beam center is the small variations in the beam centers
>> >presented: 157.5, 157.5 in the image file header,
>> >and 157.52, 157.60 in the ipmosflm script. Is the
>> >center intended to be good to a small fraction of a pixel,
>> >or good to the nearest half pixel (i.e. centered on a
>> >pixel when an integer is given, centered between
>> >pixels when a half pixel is given), or good to the
> > >nearest whole pixel (always centered on a pixel). With
>> >an even number of pixels, centered between pixels seems
>> >a likely possibility. I know I should not fuss on
>> >such small differences, but it bothers the matehmatician
>> >in me.
>> >
>> > Regards,
>> > Herbert
>> >
>> >
>> >================================================================
>> ># File Automaticaly generated by ProDC
>> ># X-Ray data collected at ESRF_ID29
>> ># Detector type: ADSC Quantum 210
>> ># Date: Thu Feb 10 19:01:18 2005
>> ># User comments: Move
>> >
>> ># Basic definitions
>> > scanner CBF
>> > gain 0.2
>> > synchrotron polar 0.99
>> > dispersion 0.0002
>> > divergence 0.001 0.001
>> > genf genfile.gen
>> >
>> ># Better have them
>> > wavelength 0.9794
>> > distance 199.43
>> > beam 157.52 157.60
>> >
>> ># Just a guess
>> > mosaic 0.234
>> >
>> ># Files
>> > directory ../
>> > template mb_LP_1_###.cbf
>> > extention cbf
>> > image 1
> > ># phi 0.00 to 1.00
>> >
>> > go
>> > ================================================
>> >
>> >
>> >=====================================================
>> > 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 Fri, 14 Apr 2006, Chris Nielsen wrote:
>> >
>> >> Hi Herb,
>> >>
>> >> Forgive the redundant question, but what is the protocol for
>> >>telling mosflm that the images
>> >> are cbf rather than adsc images? I can't dig this information out
>> >>of my email and havn't got
>> >> mosflm to run sucessfully on your latest convert_image. Your
>> >>ipmosflm input script would
>> >> be useful.
>> >>
>> >> Best, and thanks for putting up with it all,
>> >>
>> >> Chris
>> >>
>> >>
>> >> -----Original Message-----
>> >> From: Herbert J. Bernstein [mailto:yaya at bernstein-plus-sons.com]
>> >> Sent: Thu 4/13/2006 9:10 PM
>> >> To: Andrew HAMMERSLEY; Jon Wright
>> >> Cc: sweet at bnl.gov; Chris Nielsen
>> >> Subject: Re: CBFlib status
>> >>
>> >>
>> >>
>> >> I promised Chris a snapshot this evening, so before it is tomorrow,
>> >> here is the latest:
>> >>
>> >>
>> >>http://arcib.dowling.edu/~bernsteh/software/CBFlib_0.7.5_12Apr06.tar.gz
>> >>
>> >> The version of convert_image in this kit now dumps the full
>> >>image header
>> >> into a text field, which is put into
>> >>
>> >> _diffrn_data_frame.detail
>> >>
>> >> The PHI angle now seems to be set correctly. The beam center is close
>> >> (off by less than half a pixel as an index, but has the sign inverted
>> >> for the y component of the beam center in mm). I'll continue on
>> >> that tomorrow, but comments on this version would be be appreciated.
>> >>
>> >> To test, you will need to place
>> >>
>> >> mb_LP_1_001.img (Chris's adsc test case) and
>> >>
>> >> example.mar2300 (the Mar test case) into the same directory that
>> >> contains the snapshot (not into the directory it creates).
>> >> Both are available in
>> >>
>> >> http://arcib.dowling.edu/~bernsteh/software/
>> >>
>> >> then
>> >>
>> >> make all
>> >> make tests
>> >>
>> >> The manual is growing, but I still have code to write up and make
>> >> test programs for.
>> >>
>> >> Regards,
>> >> Herbert
>> >>
>> >>
>> >> --
>> >> =====================================================
>> >> Herbert J. Bernstein, Professor of Computer Science
>> >> Dowling College, Kramer Science Center, KSC 121
>> >> Idle Hour Blvd, Oakdale, NY, 11769
>> >>
>> >> Office: +1-631-244-3035
>> >> Lab (KSC 020): +1-631-244-3451
>> >> yaya at dowling.edu
>> >> =====================================================
>> >>
>> >>
>> >>
>>
>>
>> --
>> =====================================================
>> Herbert J. Bernstein, Professor of Computer Science
>> Dowling College, Kramer Science Center, KSC 121
>> Idle Hour Blvd, Oakdale, NY, 11769
>>
>> Office: +1-631-244-3035
>> Lab (KSC 020): +1-631-244-3451
>> yaya at dowling.edu
> > =====================================================
>>
>>
>>
>>
--
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
Office: +1-631-244-3035
Lab (KSC 020): +1-631-244-3451
yaya at dowling.edu
=====================================================
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