Re: [ccp4bb] pH dependent conformational change
Hi Intrinsic fluorescence may be used to monitor such change qualitatively. Another option is red-edge excitation flourescence technique may work if there are suitable fluorophores (W or F) on the each of the two domains changing solvent accessibility upon rigid body motion. Amit. On Mon, Dec 6, 2010 at 11:56 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Well, I just got word that the protein is ~100kD anyway, so I think the HSQC is out the window anyway! Jacob On Mon, Dec 6, 2010 at 12:16 PM, Roopa Thapar rtha...@hwi.buffalo.edu wrote: I agree that the experiment is a good one and can easily be done, but without assignments I think the interpretation could be ambiguous. pH dependent chemical shift perturbations could occur far removed from the linker (either due to a conformational change or the change in chemical environment around the amide nucleus) and without any information about which residues are shifting it may be difficult to conclude that these perturbations are due to a change in domain orientation rather than other subtle pH dependent effects. If there are no perturbations, then of course one can conclude little or no conformational changes occur. The magnitude of the perturbation would depend on how extensive the conformational change is. One could specifically label the protein with 15N-labeled amino acids that are particularly unique to the linker - this would simplify the spectrum and the data may be easier to interpret. It is a good experiment to try however. Roopa From: Jacob Keller [j-kell...@fsm.northwestern.edu] Sent: Monday, December 06, 2010 12:54 PM To: Roopa Thapar Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] pH dependent conformational change Even without assignments, wouldn't a dramatic shift be seen in the interacting residues? Also, I suggested the method because it is pretty easy, probably doable in a week... Jacob On Mon, Dec 6, 2010 at 11:24 AM, Roopa Thapar rtha...@hwi.buffalo.edu wrote: If there are backbone NMR assignments available then, definately a pH titration using HSQCs would give site specific information. These are easy experiments if someone can help you set them up. The perturbations should map to the inter-domain interface. If there are no assignments for the protein, spectral changes in response to pH would be harder to interpret. You could try FRET by introducing two probes - one in each domain. Roopa From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller [j-kell...@fsm.northwestern.edu] Sent: Monday, December 06, 2010 12:15 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] pH dependent conformational change Wouldn't a HSQC of 15N-labeled protein be a relatively easy yes/no experiment? Maybe it would not be incredibly definitive? Jacob On Mon, Dec 6, 2010 at 11:10 AM, Mischa Machius mach...@med.unc.edu mailto:mach...@med.unc.edu wrote: Daniel, You'll probably have to monitor pH changes through size changes of your protein, provided the structural changes will indeed cause size changes. You said easy, so that probably rules out Small-Angle X-Ray Scattering (SAXS), but that would be the highest-resolution method. You can try static and dynamic light scattering, analytical ultracentrifugation and fluorescence anisotropy. If you are really lucky, size exclusion chromatography might work too. And then there are the difficult ways... MM On Dec 6, 2010, at 11:59 AM, Daniel Jin wrote: Dear CCP4 colleagues, We have a protein that is composed of two domains connected by a short peptide linker. We have some indirect evidence showing that the two domains may somehow move against each other when exposed to different pH. It is unlikely to have any obvious secondary structure change since each domain behaves like a rigid body. I am wondering whether there is any “easy” way, biochemically or biophysically, to monitor the conformational changes in solution. Many thanks. As far as I know most of the pH sensing stories are linked to histidine residue. Can you point me to any references that show a different pH sensing mechanism (other than His)? Thanks. Best, Daniel --- Mischa Machius, PhD Director, Center for Structural Biology Assoc. Professor, Dept. of Pharmacology Member, Lineberger Comprehensive Cancer Center University of North Carolina 4079 Genetic Medicine CB#7365 120 Mason Farm Road Chapel Hill, NC 27599-7365, U.S.A. tel: +1-919-843-4485 fax: +1-919-966-5640 email: mach...@unc.edumailto:mach...@med.unc.edu -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training
[ccp4bb] MX Post-Doc postion at Diamond
Dear all, we have a vacancy for a postdoc within the MX group at Diamond. Full details can be found at http://www.diamond.ac.uk/Home/Jobs/Current/DIA0584-TH.html. Interested candidates can contact me directly by email for further details on research project associated with the post Martin PDRA, Beamline I04-1 Diamond Diamond Light Source is a new synchrotron and a leading scientific facility of its type in the world. Located on the Harwell Science and Innovation Campus in South Oxfordshire, we host facilities supporting cutting edge research in all fields of science. We are looking for a highly motivated and experienced crystallographer at the Post Doctoral Research Associate level to join the I04-1 beamline within the Macromolecular crystallography village at Diamond. I04-1 is a fixed wavelength (0.92 Å) insertion device beamline dedicated to macromolecular crystallography (MX) and complements the other four currently operating MX beamlines at Diamond. I04-1 provides a high flux X-ray beam for macromolecular structure determination by the Single Anomalous Diffraction (SAD) or Molecular replacement (MR) methods. A state of the art automated endstation consisting of a MD2 microdiffractometer, a Pilatus 2M hybrid pixel array detector and a CATS robot for automated sample handling is integrated into a automated data reduction pipeline that provides users with a high-throughput crystallography platform. Research will be focused on structural studies of a multifunctional bacterial uptake system that is required for critical mechanisms of bacterial survival in the human.
Re: [ccp4bb] pH dependent conformational change
I would like to point out that HSQC could still be applied even in such a large protein. TROSY-HSQC has been successful in improving peaks in spectra of large protein. Typically the sample would need to be deuterated to see the full effect of TROSY, but even a partial deuteration can improve signal. We have run TROSY-spectra of a complex (75kDa) with no deuteration and that spectrum is much better than a normal HSQC spectrum. Dan
Re: [ccp4bb] salt or protein crystals?
I agree - looks like small molecular diffraction. Try increasing delta-phi to catch more of the lattice to confirm - I often do a 5º image or two with the detector pushed as close as possible to check for salt diffraction when screening. The lack of low res (~15-20Å) spots around the beamstop is another smoking gun. HTH Dave David C. Briggs PhD Father, Structural Biologist and Sceptic University of Manchester E-mail: david.c.bri...@manchester.ac.uk http://manchester.academia.edu/DavidBriggs (v.sensible) http://xtaldave.wordpress.com/ (sensible) http://xtaldave.posterous.com/ (less sensible) Twitter: @xtaldave Skype: DocDCB On 7 December 2010 14:14, xiuwen zhang congru...@gmail.com wrote: Dear Colleagues, Currently we got several very tiny crystals. After exposuring a cluster of crystals one hour in home source, we could find some weak diffraction spots. As the spots are too few for indexing, I am not quite sure whether these tiny crystals are salt crystals or protein crystals. I appreciate your experience on similar case. Attached files are two diffraction images at 0 and 90 degree. Thank you very much for your kind help. Cheers, Xiuwen
[ccp4bb] BM14 Beamtime Call for Feb-March 2011.
Dear colleagues, Since January 2010, the BM14 MAD MX beamline at the ESRF (Grenoble, France) is providing beamtime for both European and Indian MX communities after a smooth transition from the UK MRC-EMBL tandem to the actual EMBL-ESRF-India consortium. The beamline is fully opened now for EU-member state and EU-associated state users[1]. Scientists are encouraged to submit proposals via the web-based eProposal interface [2] on http://www.bm14.eu (“Apply for Beamtime”). A European reviewer panel, chaired by Dr. Pedro Matias (ITQB, Lisbon, Portugal), will process the proposals and beamtime will be provided for the February – March 2011 period. *Deadline for proposal submissions*: *31st of December 2010.* Limited travel and accommodation support from the ELISA EU grant will be provided to selected users. *Beamline major features:* - 7 to 18 keV energy range with a brand new ESRF monochromator - Rayonix 225 CCD detector - MD2 Microdiffractometer with mini-Kappa goniometer head - Robotic Sample changer (SPINE sample holders) - Ultra-low resolution beamstop (down to 300 Å data recordable) - Very high resolution data collection conditions (~ 0.6 Å data recordable) - Crystal Humidity Control Device (HC1) for improving sample diffraction (* http://www.embl-grenoble.fr/groups/instr/humidifier_page1.html*)** - Remote data collection - Substantial user support during data collections Best regards, Hassan Belrhali (*belrhali-at-embl.fr*). *PS: this call is independent from Indian and ESRF calls.* [1]* EU-associated state*: Switzerland, Israel, Norway, Iceland and Liechtenstein Turkey, Croatia, the Former Yugoslav Republic of Macedonia and Serbia, Albania and Montenegro, Bosnia Herzegovina (source EC: FP7 Third Country Agreements) [2] *eProposal platform:* kindly donated by UK MRC
Re: [ccp4bb] salt or protein crystals?
Definitely small molecule crystals. You might want to push the detector closer and use better cryo solution for further confirmation. Nian On Tue, Dec 7, 2010 at 8:14 AM, xiuwen zhang congru...@gmail.com wrote: Dear Colleagues, Currently we got several very tiny crystals. After exposuring a cluster of crystals one hour in home source, we could find some weak diffraction spots. As the spots are too few for indexing, I am not quite sure whether these tiny crystals are salt crystals or protein crystals. I appreciate your experience on similar case. Attached files are two diffraction images at 0 and 90 degree. Thank you very much for your kind help. Cheers, Xiuwen
[ccp4bb] brute force MR
Hi there: The situation: We are facing difficult molecular replacement: we believe we have two molecules in the ASU, but phaser/molrep find only one. Using the electron density calculated using this single molecule, we have manually placed the 2nd molecule, albeit not good enough for rigid body refinement. Our strategy: We are looking for a program to do a 3 dimensional search around the current position of the 2nd molecule. Maybe one that calculates R-factor at the different positions, to allow to identify the correct one. ... Does anyone know of such a program, or an alternative approach? Thanks. Arnon -- *** Arnon Lavie, Professor Dept. of Biochemistry and Molecular Genetics University of Illinois at Chicago 900 S. Ashland Ave. Molecular Biology Research Building, Room 1108 (M/C 669) Chicago, IL 60607 U.S.A. Tel:(312) 355-5029 Fax:(312) 355-4535 E-mail: la...@uic.edu http://www.uic.edu/labs/lavie/ ***
Re: [ccp4bb] brute force MR
Just a thought: shave off parts of your model1, which you think might cause a clash perhaps, essentially keeping a core in place, then rerun molrep using model1 as fixed and search for a second. If you are successful, then SSM superimpose your complete model onto both and see what you have to fix the problem. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/http://web.me.com/bosch_lab/ On Dec 7, 2010, at 4:38 PM, Arnon Lavie wrote: Hi there: The situation: We are facing difficult molecular replacement: we believe we have two molecules in the ASU, but phaser/molrep find only one. Using the electron density calculated using this single molecule, we have manually placed the 2nd molecule, albeit not good enough for rigid body refinement. Our strategy: We are looking for a program to do a 3 dimensional search around the current position of the 2nd molecule. Maybe one that calculates R-factor at the different positions, to allow to identify the correct one. ... Does anyone know of such a program, or an alternative approach? Thanks. Arnon -- *** Arnon Lavie, Professor Dept. of Biochemistry and Molecular Genetics University of Illinois at Chicago 900 S. Ashland Ave. Molecular Biology Research Building, Room 1108 (M/C 669) Chicago, IL 60607 U.S.A. Tel:(312) 355-5029 Fax:(312) 355-4535 E-mail: la...@uic.edumailto:la...@uic.edu http://www.uic.edu/labs/lavie/ ***
Re: [ccp4bb] brute force MR
Try this, assuming you have good data. Use one molecule you got to do refinement (rigid body or restraint refinement with tight restraint) and phase the map. Then do a phased map molecular replacement. You might want only use the core of your protein to do the molecular replacement search to avoid the clashing problem. It worked once for me even the map was very bad. Nian On Tue, Dec 7, 2010 at 3:38 PM, Arnon Lavie la...@uic.edu wrote: Hi there: The situation: We are facing difficult molecular replacement: we believe we have two molecules in the ASU, but phaser/molrep find only one. Using the electron density calculated using this single molecule, we have manually placed the 2nd molecule, albeit not good enough for rigid body refinement. Our strategy: We are looking for a program to do a 3 dimensional search around the current position of the 2nd molecule. Maybe one that calculates R-factor at the different positions, to allow to identify the correct one. ... Does anyone know of such a program, or an alternative approach? Thanks. Arnon -- *** Arnon Lavie, Professor Dept. of Biochemistry and Molecular Genetics University of Illinois at Chicago 900 S. Ashland Ave. Molecular Biology Research Building, Room 1108 (M/C 669) Chicago, IL 60607 U.S.A. Tel: (312) 355-5029 Fax: (312) 355-4535 E-mail: la...@uic.edu http://www.uic.edu/labs/lavie/ ***
[ccp4bb] How to use XDS programme to process data collected at Q315r detector
Dear all, Recently I collected several data sets at 13B1 Taiwan beamline with Q315r detector. It's no problem to index these datasets using mosflm, but Rms residual and weighted residual is high. Here I want to try XDS to play my data. I downloaded a template example as below. !* ! Example file XDS.INP for the ADSC Q105 CCD-detector ! Characters in a line to the right of an exclamation mark are comment. !* !NOTE: XDS can handle only SMV images of TYPE=unsigned_short. ! Images are expected to be already corrected for spatial distortions. ! !Standard settings for the ADSC Q105 that rarely need to be changed DETECTOR=ADSC MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD= 65000 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 TRUSTED_REGION=0.0 1.05 !Relative radii limiting trusted detector region !UNTRUSTED_RECTANGLE= 570 1920 1469 2048 ! rectangle: X1 X2 Y1 Y2 !UNTRUSTED_ELLIPSE= 910 11101010 1210 ! ellipse enclosed by X1 X2 Y1 Y2 !File name, access, format of dark-current (non-Xray background) image !DARK_CURRENT_IMAGE=../images/blank.tif!hardly ever used !MAXIMUM_NUMBER_OF_JOBS=4 !Speeds-up COLSPOT INTEGRATE on a Linux-cluster !MAXIMUM_NUMBER_OF_PROCESSORS=4!33;ignored by single cpu version of xds !MINUTE=0 !Maximum number of minutes to wait until data image must appears !TEST=1 !Test flag. 1,2 additional diagnostics and images !NX=number of fast pixels (along X); QX=length of a X-pixel (mm) !NY=number of slow pixels (along Y); QY=length of a Y-pixel (mm) !For the ADSC, the number of detector pixels and their sizes are !obtained from the image header. It is therefore unnecessary to !specify values for NX, NY, QX, QY. !NX=2304 NY=2304 QX=0.0816 QY=0.0816 !ADSC Q4 !NX=2048 NY=2048 QX=0.0500 QY=0.0500 !ADSC Q105 !NX=2048 NY=2048 QX=0.1024 QY=0.1024 !ADSC Q210 at ESRF ID-29 !NX=4096 NY=4096 QX=0.051 QY=0.051!ADSC Q210r !NX=3072 NY=3072 QX=0.10259 QY=0.10259 !ADSC Q315 at SSRL 9-2 !NX=6144 NY=6144 QX=0.0513 QY=0.0513 !ADSC Q315r at ESRF ID-29 !AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by default !== JOB CONTROL PARAMETERS === !JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !== GEOMETRICAL PARAMETERS === !ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2 ORGX=3072.0 ORGY=3072 !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2 DETECTOR_DISTANCE= 480 !(mm) ROTATION_AXIS= 1.0 0.0 0.0 OSCILLATION_RANGE=0.5!degrees (0) X-RAY_WAVELENGTH=1.14 !Angstroem INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0 FRACTION_OF_POLARIZATION=0.90 !default=0.5 for unpolarized beam POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !=== CRYSTAL PARAMETERS = SPACE_GROUP_NUMBER=0 !0 for unknown crystals; cell constants are ignored. UNIT_CELL_CONSTANTS= 139.53 249.90 119.83 90.000 112.511 90.000 ! You may specify here the x,y,z components for the unit cell vectors if ! known from a previous run using the same crystal in the same orientation !UNIT_CELL_A-AXIS= !UNIT_CELL_B-AXIS= !UNIT_CELL_C-AXIS= !Optional reindexing transformation to apply on reflection indices !REIDX= 0 0 -1 0 0 -1 0 0 -1 0 0 0 !FRIEDEL'S_LAW=FALSE !Default is TRUE. However indexed cell parameter for a b and c is small and error information indicates that cell solution is not accurate. I suspect that I need to change some input parameters besides selection of ORGX=3072.0 ORGY=3072 when using XDS as the template is for ADSC Q105. Here I want to know if anyone has experience to use XDS to process data collected at Q315r and what error I made for using this script. Thank you very much for any suggestion. Best regards, Donghui
Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector
Look into the header of your image file via more or run mosflm on one image and look at the output in the terminal window. You'll get the pixelsize and you'll need to convert the beamcenter into pixels from mosflm. Keep in mind that beam X = orgy in xds and beam y is orgx Plus the usual stuff lambda distance 2theta Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Dec 7, 2010, at 22:03, wu donghui wdh0...@gmail.com wrote: Dear all, Recently I collected several data sets at 13B1 Taiwan beamline with Q315r detector. It's no problem to index these datasets using mosflm, but Rms residual and weighted residual is high. Here I want to try XDS to play my data. I downloaded a template example as below. !* ! Example file XDS.INP for the ADSC Q105 CCD-detector ! Characters in a line to the right of an exclamation mark are comment. !* !NOTE: XDS can handle only SMV images of TYPE=unsigned_short. ! Images are expected to be already corrected for spatial distortions. ! !Standard settings for the ADSC Q105 that rarely need to be changed DETECTOR=ADSC MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD= 65000 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 TRUSTED_REGION=0.0 1.05 !Relative radii limiting trusted detector region !UNTRUSTED_RECTANGLE= 570 1920 1469 2048 ! rectangle: X1 X2 Y1 Y2 !UNTRUSTED_ELLIPSE= 910 11101010 1210 ! ellipse enclosed by X1 X2 Y1 Y2 !File name, access, format of dark-current (non-Xray background) image !DARK_CURRENT_IMAGE=../images/blank.tif!hardly ever used !MAXIMUM_NUMBER_OF_JOBS=4 !Speeds-up COLSPOT INTEGRATE on a Linux-cluster !MAXIMUM_NUMBER_OF_PROCESSORS=4!33;ignored by single cpu version of xds !MINUTE=0 !Maximum number of minutes to wait until data image must appears !TEST=1 !Test flag. 1,2 additional diagnostics and images !NX=number of fast pixels (along X); QX=length of a X-pixel (mm) !NY=number of slow pixels (along Y); QY=length of a Y-pixel (mm) !For the ADSC, the number of detector pixels and their sizes are !obtained from the image header. It is therefore unnecessary to !specify values for NX, NY, QX, QY. !NX=2304 NY=2304 QX=0.0816 QY=0.0816 !ADSC Q4 !NX=2048 NY=2048 QX=0.0500 QY=0.0500 !ADSC Q105 !NX=2048 NY=2048 QX=0.1024 QY=0.1024 !ADSC Q210 at ESRF ID-29 !NX=4096 NY=4096 QX=0.051 QY=0.051!ADSC Q210r !NX=3072 NY=3072 QX=0.10259 QY=0.10259 !ADSC Q315 at SSRL 9-2 !NX=6144 NY=6144 QX=0.0513 QY=0.0513 !ADSC Q315r at ESRF ID-29 !AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by default !== JOB CONTROL PARAMETERS === !JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !== GEOMETRICAL PARAMETERS === !ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2 ORGX=3072.0 ORGY=3072 !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2 DETECTOR_DISTANCE= 480 !(mm) ROTATION_AXIS= 1.0 0.0 0.0 OSCILLATION_RANGE=0.5!degrees (0) X-RAY_WAVELENGTH=1.14 !Angstroem INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0 FRACTION_OF_POLARIZATION=0.90 !default=0.5 for unpolarized beam POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !=== CRYSTAL PARAMETERS = SPACE_GROUP_NUMBER=0 !0 for unknown crystals; cell constants are ignored. UNIT_CELL_CONSTANTS= 139.53 249.90 119.83 90.000 112.511 90.000 ! You may specify here the x,y,z components for the unit cell vectors if ! known from a previous run using the same crystal in the same orientation !UNIT_CELL_A-AXIS= !UNIT_CELL_B-AXIS= !UNIT_CELL_C-AXIS= !Optional reindexing transformation to apply on reflection indices !REIDX= 0 0 -1 0 0 -1 0 0 -1 0 0 0 !FRIEDEL'S_LAW=FALSE !Default is TRUE. However indexed cell parameter for a b and c is small and error information indicates that cell solution is not accurate. I suspect that I need to change some input parameters besides selection of ORGX=3072.0 ORGY=3072 when using XDS as the template is for ADSC Q105. Here I want to know if anyone has experience to use XDS to process data collected at Q315r and what error I made for using this script. Thank you very much for any suggestion. Best regards, Donghui
Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector
Donghui, there are several ways to get ORGX ORGY parameters. As Juergen suggested, you could use the numbers from the header or Mosflm output. More information on the excellent XDS Wiki: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Obtaining_ORGX_ORGY Another option would be to run generate_XDS.INP script, which will get ORGX ORGY parameters from headers automatically: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP If you know the spacegroup, define it with keyword SPACE_GROUP_NUMBER= (your script has 0). HTH, Konstantin On Wed, 8 Dec 2010, wu donghui wrote: Dear all, Recently I collected several data sets at 13B1 Taiwan beamline with Q315r detector. It's no problem to index these datasets using mosflm, but Rms residual and weighted residual is high. Here I want to try XDS to play my data. I downloaded a template example as below. ! * ! Example file XDS.INP for the ADSC Q105 CCD-detector ! Characters in a line to the right of an exclamation mark are comment. ! * !NOTE: XDS can handle only SMV images of TYPE=unsigned_short. ! Images are expected to be already corrected for spatial distortions. ! !Standard settings for the ADSC Q105 that rarely need to be changed DETECTOR=ADSC MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD= 65000 DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 TRUSTED_REGION=0.0 1.05 !Relative radii limiting trusted detector region !UNTRUSTED_RECTANGLE= 570 1920 1469 2048 ! rectangle: X1 X2 Y1 Y2 !UNTRUSTED_ELLIPSE= 910 1110 1010 1210 ! ellipse enclosed by X1 X2 Y1 Y2 !File name, access, format of dark-current (non-Xray background) image !DARK_CURRENT_IMAGE=../images/blank.tif !hardly ever used !MAXIMUM_NUMBER_OF_JOBS=4 !Speeds-up COLSPOT INTEGRATE on a Linux-cluster !MAXIMUM_NUMBER_OF_PROCESSORS=4!33;ignored by single cpu version of xds !MINUTE=0 !Maximum number of minutes to wait until data image must appears !TEST=1 !Test flag. 1,2 additional diagnostics and images !NX=number of fast pixels (along X); QX=length of a X-pixel (mm) !NY=number of slow pixels (along Y); QY=length of a Y-pixel (mm) !For the ADSC, the number of detector pixels and their sizes are !obtained from the image header. It is therefore unnecessary to !specify values for NX, NY, QX, QY. !NX=2304 NY=2304 QX=0.0816 QY=0.0816 !ADSC Q4 !NX=2048 NY=2048 QX=0.0500 QY=0.0500 !ADSC Q105 !NX=2048 NY=2048 QX=0.1024 QY=0.1024 !ADSC Q210 at ESRF ID-29 !NX=4096 NY=4096 QX=0.051 QY=0.051 !ADSC Q210r !NX=3072 NY=3072 QX=0.10259 QY=0.10259 !ADSC Q315 at SSRL 9-2 !NX=6144 NY=6144 QX=0.0513 QY=0.0513 !ADSC Q315r at ESRF ID-29 !AIR=0.001 !Air absorption coefficient of x-rays is computed by XDS by default !== JOB CONTROL PARAMETERS === !JOB= XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT !== GEOMETRICAL PARAMETERS === !ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2 ORGX=3072.0 ORGY=3072 !Detector origin (pixels). ORGX=NX/2; ORGY=NY/2 DETECTOR_DISTANCE= 480 !(mm) ROTATION_AXIS= 1.0 0.0 0.0 OSCILLATION_RANGE=0.5 !degrees (0) X-RAY_WAVELENGTH=1.14 !Angstroem INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0 FRACTION_OF_POLARIZATION=0.90 !default=0.5 for unpolarized beam POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0 !=== CRYSTAL PARAMETERS = SPACE_GROUP_NUMBER=0 !0 for unknown crystals; cell constants are ignored. UNIT_CELL_CONSTANTS= 139.53 249.90 119.83 90.000 112.511 90.000 ! You may specify here the x,y,z components for the unit cell vectors if ! known from a previous run using the same crystal in the same orientation !UNIT_CELL_A-AXIS= !UNIT_CELL_B-AXIS= !UNIT_CELL_C-AXIS= !Optional reindexing transformation to apply on reflection indices !REIDX= 0 0 -1 0 0 -1 0 0 -1 0 0 0 !FRIEDEL'S_LAW=FALSE !Default is TRUE. However indexed cell parameter for a b and c is small and error information indicates that cell solution is not accurate. I suspect that I need to change some input parameters besides selection of ORGX=3072.0 ORGY=3072 when using XDS as the template is for ADSC Q105. Here I want to know if anyone has experience to use XDS to process data collected at Q315r and what error I made for using this script. Thank you very much for any suggestion. Best regards, Donghui -- Konstantin Korotkov, Ph.D. Research Scientist University of Washington Department of Biochemistry Box 357742 Seattle, WA 98195-7742 (206)616-4512 k...@u.washington.edu --
[ccp4bb] superposing (hkl) indexes on diffraction image
Dear all, I would like to make a picture of diffraction photograph with (hkl) indexes. I found it in Fig. 1 in the paper: Acta Cryst. (2009). D65, 553-559 http://dx.doi.org/10.1107/S0907444909010725 Direct link to the figure: http://journals.iucr.org/d/issues/2009/06/00/dz5158/dz5158fig1.html Can LABELIT, Mosflm or other program make image file (jpg or something) such like that? Thank you very much in advance, K. Yamashita
