[Imgcif-l] RE: CBFlib status
Harry Powell harry at mrc-lmb.cam.ac.ukMon Apr 17 22:44:29 BST 2006
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Hi I've put a copy of mosflm with the patch on our anonymous ftp site - it's the "build-it-yourself" version without REFIX indexing; ftp ftp.mrc-lmb.cam.ac.uk anonymous <your username> cd /pub/incoming/mosflm bin get herb.gz bye then gunzip it and ./build should work on most modern boxes (except those using gfortran...) > 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 > ===================================================== > _______________________________________________ > imgcif-l mailing list > imgcif-l at iucr.org > http://scripts.iucr.org/mailman/listinfo/imgcif-l > Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
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