[ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
-- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 7:07 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr marcin.woj...@diamond.ac.uk Dear Marcin, Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no But indicating that the C compiler does not work. I will try Fortran compiler shortly and let you know. Best, Donghui On Mon, Mar 3, 2014 at 5:43 PM, Marcin Wojdyr marcin.woj...@diamond.ac.ukwrote: On Mon, Mar 03, 2014 at 01:16:37PM +0800, wu donghui wrote: gcc version in my Mac OS X 10.8.5 is as below. Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) That's Apple compiler. It supports C and C++ but not Fortran, so you also need a Fortran compiler such as gfortran. checking for gcc... gcc-4.2.1 checking whether the C compiler works... no Did you set CC=gcc-4.2.1? Marcin -- 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
[ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
-- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin
Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5
Dear Tim, Here I attached the config.log file for your help. I have tried to use either gcc-4.2.1 (Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1), or g++-4.2.1(/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1) or gfortran-4.8.1 compiler. Still same error appeared as attached from the config.log file. Thanks for your attention. Best, Donghui On Mon, Mar 3, 2014 at 11:02 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Donghui, did you already take a look into config.log to read the error message why your gcc-compiler does not work? You should start at the end of the log file and scroll backwards until you find the error message. Best, Tim On 03/03/2014 03:51 PM, wu donghui wrote: -- Forwarded message -- From: wu donghui wdh0...@gmail.com Date: Mon, Mar 3, 2014 at 10:44 PM Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5 To: Marcin Wojdyr woj...@gmail.com Dear Marcin, The reason that I want to build from source is that running ipmosflm can not be done from binary code, while binary code only supports imosflm running. Thanks. Best, Donghui On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote: Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. As is shown, it can identify gcc for gcc-4.2.1 checking for gcc... gcc-4.2.1 checking whether the C compiler works... no To me it looks that you set compiler to non-existent gcc-4.2.1, so it doesn't work. Do you have a reason to build CCP4 from source? There are binaries available for OSX. Best regards Marcin - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTFJl9UxlJ7aRr7hoRAo/PAJwLSzdU2Undrc0tosdeSSpdC1aSxACgvzUP khM2NeDGueN6Saat/3kZ+iU= =Z6Ci -END PGP SIGNATURE- config.log Description: Binary data
[ccp4bb] Off topic about program for multiple protein sequence alignment
Dear all, I want to know your suggestions about current protein sequence alignment programs. It seems that different programs give different alignment results such as from analysis of Clustal W and MULTALIN. Thanks for any input or comments. Best regards, Donghui
[ccp4bb] A script is needed to renumber image
Dear all, I need a script to renumber my image. My initial image number ranges from *_1081.img to *_1440.img. There are 360 images in total. I want to renumber these images with the ranges from *_361.img to *_720.img, that means every initial image-720, but I don't know how to do it. Below is my script draft. #! /bin/csh -f @ i = 1081 while ( $i = 1081 ) while ($i = 1440 ) echo mv CD267A_3_pk_1_$i.img CD267A_3_pk_1_$i-720.img @ i++ end exit Can anyone help me for this script? Thank you very much. Best regards, Donghui
Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector
Dear all, Thank you very much for your valuable inputs. This is an update based from the suggestions. Following Pierre's suggestion, I installed xdsme ( http://code.google.com/p/xdsme/) and run it. xdsme extracts image header as the below: Image format: adsc Detector type: ADSC 315 Detector distance: 480.00 mm X-ray wavelength:1.1397 A Oscillation range: 0.5000 degree Beam coordinate X: 1535.3 pixel Y: 1535.3 pixel As the detector type should be ADSC 315r, the indexing shows warning information that !!! WARNING in IDXREF. Solution is inaccurate. Based on Miles's suggestion, I run the program adxv ( http://www.scripps.edu/~arvai/adxv.html) to extract image header as the below: Distance 480.000 mm Pixel Size 0.10259 mm Wavelength 1.13967 A Beam Center X: 1535 pixels Y: 1536 pixels OSC_RANGE 0.5000 degree However the beam center pixel seems to indicate that ccd detector is Q315 but not Q315r based on the provided template script from XDS website 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 In summary, I can not index my data collected at Q315r Taiwan 13B1 beamline using XDS program. It seems that XDS process data from Q315 is more efficient that from Q315r. Any suggestions will be much appreciated. Best regards, Donghui On Wed, Dec 8, 2010 at 11:03 AM, 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
Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector
Marian, It seems that XDS does matter detector type Q315 or Q315r. Same crystals when collected at ESRF Beamline 23-1 using Q315 detector can be processed straightly with the provided script from XDS website and I only need to input ORGX=1536.0 ORGY=1536.0 for indexing or data integration. If XDS does not matter Q315 or Q315r, the indexing of data from Q315r should be as clear as from Q315 collected at ESRF beamline 23-1. But XDS can not index the data from Q315r correctly. Best regards, Donghui * ! 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=1536.0 ORGY=1536.0 !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. On Wed, Dec 8, 2010 at 11:05 PM, Marian Szebenyi dm...@cornell.edu wrote: Donghui, The Q315r and Q315 have the same format, so for the XDS input it does not matter whether you have a Q315 or Q315r. What does matter is whether the data were collected in binned or unbinned mode. For binned, the number of pixels is 3072 and the pixel size is 0.10259 mm. For unbinned, the number of pixels is 6144 and the pixel size is 0.0513. In your case, the file header tells you that you have binned data, with 3072 x 3072 pixels and a pixel size of 0.10259, and this is the information you need to give XDS. Yours, Marian Szebenyi MacCHESS wu donghui wrote: Dear all, Thank you very much for your valuable inputs. This is an update based from the suggestions. Following Pierre's suggestion, I installed xdsme (http://code.google.com/p/xdsme/) and run it. xdsme extracts image header as the below: Image format: adsc Detector type: ADSC 315 Detector distance: 480.00 mm X-ray wavelength:1.1397 A Oscillation range: 0.5000 degree Beam coordinate X: 1535.3 pixel Y: 1535.3 pixel As the detector
Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector
Dear Bosch, Ye, at the moment, I don't know if the geometry of my beamline 13B1 at Taiwan take the same direction as in the script. How can I get this information? Directly ask beamline scientists at Taiwan? or if there is some log files which may contain such information during data collection. Thank you very much. DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 Best regards, Donghui On Thu, Dec 9, 2010 at 12:07 AM, Bosch, Juergen jubo...@jhsph.edu wrote: Thanks Tim, our mails must have crossed :-) @ Donghui: This is the standard JOB card JOB= ALL !XYCORR INIT COLSPOT IDXREF DEFPIX XPLAN INTEGRATE CORRECT what you probably need is after running the first time xds in the directory to go back into your script and change it into JOB=DEFPIX XPLAN INTEGRATE CORRECT And also change the space group and unit cell according to the output in IDXREF.LP Jürgen Alternatively is the geometry of your beamline the same as in the script ? DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0 DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0 - 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 8, 2010, at 10:41 AM, Tim Gruene wrote: Dear Donghui, only because XDS shows a warning about an inaccurate solution does not necessarily mean that it did not index your data correctly. Check the file IDXREF.LP (from bottom to top - log-file are usually more interesting that way round). There should be a summary of the refined values and also a listing of the number of spots XDS could index based on that solution. If the detector distance was NOT refined to a value to far from what it really was and if the number of indexed spots, say, about 40-50% of the total number of spots, just carry on an see whether XDS does not 'click in' to the correct solution. You carry on be going to the JOB-card in XDS.INP and delete all entries before DEFPIX You find an example of what I am talking about at the XDS wiki at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Tutorial(First_Steps) Maybe this helps, Tim On Wed, Dec 08, 2010 at 10:53:33PM +0800, wu donghui wrote: Dear all, Thank you very much for your valuable inputs. This is an update based from the suggestions. Following Pierre's suggestion, I installed xdsme ( http://code.google.com/p/xdsme/) and run it. xdsme extracts image header as the below: Image format: adsc Detector type: ADSC 315 Detector distance: 480.00 mm X-ray wavelength:1.1397 A Oscillation range: 0.5000 degree Beam coordinate X: 1535.3 pixel Y: 1535.3 pixel As the detector type should be ADSC 315r, the indexing shows warning information that !!! WARNING in IDXREF. Solution is inaccurate. Based on Miles's suggestion, I run the program adxv ( http://www.scripps.edu/~arvai/adxv.html) to extract image header as the below: Distance 480.000 mm Pixel Size 0.10259 mm Wavelength 1.13967 A Beam Center X: 1535 pixels Y: 1536 pixels OSC_RANGE 0.5000 degree However the beam center pixel seems to indicate that ccd detector is Q315 but not Q315r based on the provided template script from XDS website 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
Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector
Dear all, Following Pierre and Harry's suggestion, problem solved using xdsme -i 'ROTATION_AXIS= -1.0 0.0 0.0' image_name_*.img. Thank you very much. Good luck for everyone Cheers, Donghui On Thu, Dec 9, 2010 at 12:39 AM, LEGRAND Pierre pierre.legr...@synchrotron-soleil.fr wrote: Hi again, One last comment, following Harry's suggestion, if the phi axis turns in the revers order, for xdsme and xds you will need the following command: xdsme -i 'ROTATION_AXIS= -1.0 0.0 0.0' image_name_*.img Good luck, Pierre -Original Message- From: CCP4 bulletin board on behalf of wu donghui Sent: Wed 12/8/2010 4:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to use XDS programme to process data collected at Q315r detector Marian, It seems that XDS does matter detector type Q315 or Q315r. Same crystals when collected at ESRF Beamline 23-1 using Q315 detector can be processed straightly with the provided script from XDS website and I only need to input ORGX=1536.0 ORGY=1536.0 for indexing or data integration. If XDS does not matter Q315 or Q315r, the indexing of data from Q315r should be as clear as from Q315 collected at ESRF beamline 23-1. But XDS can not index the data from Q315r correctly. Best regards, Donghui * ! 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=1536.0 ORGY=1536.0 !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. On Wed, Dec 8, 2010 at 11:05 PM, Marian Szebenyi dm...@cornell.edu wrote: Donghui, The Q315r and Q315 have the same format, so for the XDS input it does not matter whether you have a Q315 or Q315r. What does matter is whether the data were collected in binned or unbinned mode. For binned, the number of pixels is 3072 and the pixel size is 0.10259 mm. For unbinned, the number
[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 optimize crystallization of a membrane proteinf
It does not look like protein crystal and IZIT staining is not reliable in determining protein or other. Mostly it is like detergent or PEG crystal or quasi-crystal. Good luck Wu 2010/8/31 qiangm zhang zhangqia...@gmail.com Hi all, I got a crystal of one membrane protein (~60kD) from Na/K phosphate condition (see getit_4), then I got the improved crystal like getit_5 after trying seeding, different detergents, lipids and additives. But this crystal does not diffract at all, I already tried Izit staining which shows it is protein crystal (detergent crystal?). Does anyone have any good suggestions for the optimization of this membrane protein crystallization? Thank you in advance. Best regards Qiangmin Zhang Biomedical Science Tower 3 Room1034 3501 Fifth Avenue Pittsburgh, PA 15260 -- 张强敏
[ccp4bb] bug report of SHARP 2.6.0 Sushi 3.8.0
Hi ccp4ers, I found a problem when I used SHARP 2.6.0 Sushi 3.8.0 to search new heavy atom sites from 2 identified sites from SnB. Sharp can output new identified site lists however with all new identified sites set distance at zero with the 2 sites and strangely the 2 sites all output as G0 site. Similarly problem has been found by other colleagues in my lab. Best regards, Donghui
[ccp4bb] About seeding in microbatch under oil crystallization
Hi ccp4bbers, I want to know if anyone has any experience about seeding (streak seeding or microseeding) in microbatch under oil crystallization. I wonder if the oil might block or wipe away the seeds if cat whisker is used for streak seeding. Thank you for your input ahead. Best regards, Donghui
Re: [ccp4bb] About seeding in microbatch under oil crystallization
Dear Patrick, I have Oryx robot in our lab. I got my initial crystallization hit from sitting drop vapor diffusion method. This hit can be reproduced by sitting drop through spontaneous nucleation with many tiny crystals after around 1 week but seeding into sitting drop failed and I found once I opened slide and let the drop exposed to air even for a few second, it will turn turbid instantly and I think this might be the reason why seeding in sitting drop is not workable as most protein precipitated and protein concentration dropped very low and seeds implanted inside might be dissolved quickly even after certain periods of equilibration before seeding. That is the reason I want to seperate my drop from air by adding oil on it and then try seeding under oil. Also microbatch under oil might prevent skin formation and maintain protein concentraiton at relatively high level to support seed crystal growth. Best regards, Donghui On Wed, May 19, 2010 at 7:37 PM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: Dear Donghui I can confirm that microseeding with microbatch-under-oil works fine. It’s one of our standard set of scripts. Our Oryx robots use contact dispensing (the tip touches the plate) so the seeds can be added very reliably as a suspension. Several users have reported that the method works, although I don’t know of anyone who has made a statistical comparison between Sitting Drop and Microbatch. I would expect them to be about the same. Do you have an Oryx or some other robot? And was there any particular reason why you want to use microbatch? Best wishes Patrick -- For information and discussion about protein crystallization and automation, please join our bulletin board at http://groups-beta.google.com/group/oryx_group?hl=en patr...@douglas.co.ukDouglas Instruments Ltd. DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk/ Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On Behalf Of *wu donghui *Sent:* 19 May 2010 10:29 *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] About seeding in microbatch under oil crystallization Hi ccp4bbers, I want to know if anyone has any experience about seeding (streak seeding or microseeding) in microbatch under oil crystallization. I wonder if the oil might block or wipe away the seeds if cat whisker is used for streak seeding. Thank you for your input ahead. Best regards, Donghui
Re: [ccp4bb] Help with MR in P21
Two cents are added here. First, try P2 as somethimes systematic absence along b axis is misleading due to weak diffraction or pseduo translation. Second, try P1. Good luck, Donghui On Tue, Jan 26, 2010 at 1:50 AM, Michele Lunelli efu...@yahoo.it wrote: Dear all, I am trying to solve a structure at 2.05 A resolution by molecular replacement. The space group seems to be P21, with unit cell dimension 52.63, 29.43, 104.970 and beta = 95.60. Only one copy of the protein should be present in the asymmetric unit, with 58% of solvent content. The search model used for MR is a truncated construct of the same protein, comprising more that 60% of the residues. However, no convincing MR solution is found (I used phaser, molrep, epmr and also mr.bump). No solutions refine to R and Rfree lower than 51-52%. The CCP4 documentation about twinning states that Monoclinic with na + nc ~ a or na + nc ~ c can be twinned. This is not clear to me, but I have c = 2a, and therefore n = 2/3. Nevertheless all the tests run by ctruncate (and sfcheck) exclude twinning. The observed cumulative distribution for |L| almost overlap the expected untwinned, and the observed cumulative intensity distribution is not sigmoidal at all (actually it is growing faster that the theoretical). Also the acentric and centric moments exclude twinning, for example the acentric: E = 0.858 (Expected value = 0.886, Perfect Twin = 0.94) E**3 = 1.442 (Expected value = 1.329, Perfect Twin = 1.175) E**4 = 2.438 (Expected value = 2, Perfect Twin = 1.5) Both ctruncate and sfcheck found a pseudo-translation vector: ctruncate (0.050, 0.000, 0.957), ratio 0.23 sfcheck (0.954, 0.000, 0.040), ratio 0.218 However a second copy cannot be present in the asymmetric unit (there would be 16% of solvent content). Since the protein is expected to form a coiled-coil, I think that the detected pseudo-translation arises from the helices. Alternatively, it is possible that the space group is wrong? And if so, how can I figure out the correct one? Thank you in advance, Michele
[ccp4bb] How to model apo protein structure from solved ligand bound high resolution structure?
Dear CCP4ers, Recently we have solved two structures from E.coli in high resolution, which have bound two different ligands tightly already. Here I want to know if there is any program which can let us model the structure of our apo proteins confidently. Thanks ahead for any comment and input. Regards, Donghui
Re: [ccp4bb] How to model apo protein structure from solved ligand bound high resolution structure?
More information about the two ligand bound structures, each protein is composed of two globular domains, between the two globular domains, there lies a deep cleft and ligand sits or buried there comfortably. These two domains are connected by a hinge region, here we want to model how this hinge region moves upon ligand binding. Any recommendation for any program which can do this task well. Thanks ahead. Donghui On Sun, Aug 9, 2009 at 8:37 PM, wu donghui wdh0...@gmail.com wrote: Dear CCP4ers, Recently we have solved two structures from E.coli in high resolution, which have bound two different ligands tightly already. Here I want to know if there is any program which can let us model the structure of our apo proteins confidently. Thanks ahead for any comment and input. Regards, Donghui
Re: [ccp4bb] Question about Phoenix crystallization robot
Diana, We already got a new Art Robbins Phoenix crystallization robot recently and very friendly as time consuming per plate is concerned. Theoretically your strategy of aspirating one sample enough and dispensing into several 96 well plate is feasible. However it should depend on the protocol set by this company. It seems there is no such protocol incorporated in their software, so it should be difficult to do this. Anyway you should contact the company directly for such information. HTH Donghui On 4/25/08, Diana Tomchick [EMAIL PROTECTED] wrote: BACKGROUND: Recently we acquired an Art Robbins Phoenix crystallization robot. This instrument is in a shared environment, accessible to labs with projects that range from small, well-behaved soluble cytosolic proteins to large complexes and integral membrane proteins. Many of our users obtain only small quantities (a few hundred microliters) of purified proteins, and they are always looking for ways to maximize the number of crystallization screens they can set up with their samples. QUESTION: Several users have recently asked if they could use a protocol that allows them to aspirate enough protein into the Nanoneedle (the needle used for dispensing protein) to set up 3-5 or more different 96-condition screens. They feel this would minimize any sample waste and maximize their time. Our concern is that this might result in clogging of the Nanoneedle due to evaporation and subsequent precipitation of their protein, as the amount of time required for such a protocol would be greater than 10 minutes. Our local Art Robbins representative has agreed with us that this is not a recommended protocol. We are in a bit of a dilemma as we do not have enough experience with this robot to definitively say that the users should not follow this kind of protocol, but perhaps there is a better way to achieve their desired goal. Does anyone out there have any practical suggestions and experience that could help us accommodate such user requests? Thank you in advance, I'll post a summary of responses, Diana * * * * * * * * * * * * * * * * * * * * * * * * * * * * Diana R. Tomchick Associate Professor University of Texas Southwestern Medical Center Department of Biochemistry 5323 Harry Hines Blvd. Rm. ND10.214B Dallas, TX 75390-8816, U.S.A. Email: [EMAIL PROTECTED] 214-645-6383 (phone) 214-645-6353 (fax)
Re: [ccp4bb] Optimization of needle crystals?
You might have to test if it is salt/detergent or protein crystal first. If it is really protein crystal, never give up and for needle crystal, generally it is difficult to optimze, however in most cases, the diffraction is well enough. If it is protein crystal, as some researcher has mentioned, first try Hampton additive screening, if you are lucky, you might get an additive condition which might improve the thickness of needle or plate to some thickness, if additive screening does not improve much to your protein crystal, you have to try seeding. HTH Donghui On 4/16/08, Ngo Duc Tri [EMAIL PROTECTED] wrote: Dear ccp4 users, I crystallized a membrane protein and got some conditions showing the small needle crystals. All condition contained Mg2+ and high buffer pH. I learn that it is difficult to optimize the needle crystal. However I would like to ask your experience how to optimize in this case. Here is the attached picture of my crystal. Thank you very much for your advices! My best regards, TriNgo PhD Student - Sungkyunkwan University, Korea
Re: [ccp4bb] protein expression
Hi Chen, In this case, it seems that linker region is of great importance for the proper folding of the two linked domains. I have not much experience in linker region design, generally use (GS)5-10 times. However it depends on individual case. Anyone who has successful experience in linker region design might share your success with others. Thanks a lot. Regards, Donghui On 3/5/08, Daniel Jin [EMAIL PROTECTED] wrote: Hi, I have a protein with two independently folded domains. I can express either one in bacteria with pretty good expression yield. However, when I put them together with a linker, the expression drops significantly. I can barely see any soluble protein and most of it is now inclusion bodies. I used the same bacteria strain and expression/purification conditions. Is it normal? Any suggestion about how to improve? Many thanks. Best, Chen -- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
[ccp4bb] Off topic: ask about cryoprotectant selection using lithium sulfate as precipitant for crystal growth
Dear all, Recently, I got a crystallization condition as 0.1 M Bis tris ph 6.5, 1.3Mlithium sulfate, 0.1M NaCl, the shape of crystals is needle cluster, very difficult to grow bigger, microseeding does not work, then I tried macroseeding, and found crystal can grow bigger and rod like. However as for the cryoprotectant, crystal will dissolve in glycerol, ethylene glycol, MPD and PEG, even in the very low concentration about 5%. I found my crystal can grow under the additive 2-propanol in addition to the above mentioned crystallization condition. I also noticed that Hampton cryoprotectant kit has the 2-propanol as cryoprotectant. I want to know if anyone have ever used 2-propanol as the cryoprotectant and what effect it might be. By the way Hampton also mention lithium sulfate can be used as cryoprotectant, the recommended maxium concentration is 2M, I tried and found ice ring is severe and it is very easily to form lithium sulfate salt crystal at this high concentration, I also tried sodium malonate, the diffraction gave me few spots, resolution is only about 6--7 angstrom. Does anyone encounter such problem by lithium sulfate? Welcome to any replies. Thanks a lot in advance. Donghui
Re: [ccp4bb] Off topic: ask about cryoprotectant selection using lithium sulfate as precipitant for crystal growth
Dear Lokesh, Actually I have tried to dip my crytal directly into mineral oil, no ice ring, but also no diffraction, which might indicate crystal packing under mineral oil is not stable. Anyway, thanks a lot for your valuable information. Other friends mention the use of LiCl or Lithium formate as cryoprotectant, I will try these immediately and will let you know if it works. Best regards, Donghui On 2/27/08, Lokesh Gakhar [EMAIL PROTECTED] wrote: Hi Donghui, Have you tried mineral oil? That has sometimes worked for us when other cryoprotectants have given problems. -Lokesh On Tue, Feb 26, 2008 at 9:30 PM, wu donghui [EMAIL PROTECTED] wrote: Dear all, Recently, I got a crystallization condition as 0.1 M Bis tris ph 6.5, 1.3M lithium sulfate, 0.1M NaCl, the shape of crystals is needle cluster, very difficult to grow bigger, microseeding does not work, then I tried macroseeding, and found crystal can grow bigger and rod like. However as for the cryoprotectant, crystal will dissolve in glycerol, ethylene glycol, MPD and PEG, even in the very low concentration about 5%. I found my crystal can grow under the additive 2-propanol in addition to the above mentioned crystallization condition. I also noticed that Hampton cryoprotectant kit has the 2-propanol as cryoprotectant. I want to know if anyone have ever used 2-propanol as the cryoprotectant and what effect it might be. By the way Hampton also mention lithium sulfate can be used as cryoprotectant, the recommended maxium concentration is 2M, I tried and found ice ring is severe and it is very easily to form lithium sulfate salt crystal at this high concentration, I also tried sodium malonate, the diffraction gave me few spots, resolution is only about 6--7 angstrom. Does anyone encounter such problem by lithium sulfate? Welcome to any replies. Thanks a lot in advance. Donghui
[ccp4bb] Why there is no C21 space group in crystal system
Dear all, I just get into touch with x-ray crystallography, and I made a big discovery that there is no C21 space group in monoclinic system, which system only contains P2, P21 and C2 groups. Even in the entire 65 chiral space group, there is no space for this group. I made an assumption that if there is C21 space group in monoclinic system, then the four equivalent point position could be described as: x, y, z; 1/2+x, 1/2+y, z; -x, 1/2+y, -z; 1/2-x, y, -z. However when I check the 65 chiral space group, no one is compatible with this equivalent positions. And I know I must make some mistakes. Unfortunately I can not find where the mistake stems from. I have to recourse to our expert community for your generous help. All replies are warmly welcomed and appreciated. Best regards, Donghui
