[ccp4bb] CAD on multi-record file
Dear all, (apologies for those being tired of similar questions...) I have tried using CAD on an unscaled MTZ from Mosflm. All I wanted to do was to change crystal name, dataset name and project name. This is what I got: - BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: CAD version 6.1 : 20/01/09## ### User: unknown Run date: 9/ 4/2009 Run time: 16:20:40 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B Data line--- TITLE Changing crystal, dataset and project names Data line--- LABIN FILE_NUMBER 1 ALL Data line--- DPNAME FILE_NUMBER 1 New New NONISO Data line--- DRENAME FILE_NUMBER 1 New New Insulin_01 Dataset_01 Data line--- END No CTYP lines input for file: 1 Indices output even if all data items flagged missing Warning, NOT all LABOUT data lines given OPENED INPUT MTZ FILE Logical Name: HKLIN1 Filename: exp_01/in1_MS_1_001.mtz * Title: Untitled * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 New New New 81.6000 81.6000 33.6000 90. 90. 120. 0.92000 * Number of Columns = 18 * Number of Reflections = 40898 * Missing value set to NaN in input mtz file * Number of Batches = 100 * Column Labels : H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS * Column Types : H H H Y B J Q J Q R R R R R R I I R * Associated datasets : 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 81.6000 81.6000 33.6000 90. 90. 120. * Resolution Range : 0.001090.32315 ( 30.345 - 1.759 A ) * Sort Order : 0 0 0 0 0 * Space group = 'H3' (number 146) File 1 is a multi-record MTZ file. Inputting a multi-record file to CAD is an unmitigated disaster! Please use MTZUTILS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- CAD: Input file is unmerged MTZ file. CAD: Input file is unmerged MTZ file. Times: User: 0.1s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B -- So it would appear that CAD is no good for this sort of files. What should I use, then? I have tried looking into mtzutils, but I don't see how to do it. Anyone for help? J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk web page:
Re: [ccp4bb] CAD on multi-record file
Hi James, This isn't a direct answer to your question, but you can assign these on the Scala command line input, thus: name run 1 project AUTOMATIC crystal DEFAULT dataset WAVE1 name run 2 project AUTOMATIC crystal DEFAULT dataset WAVE2 I am assuming that this would be your next step anyhow. Best wishes, Graeme 2009/4/9 James Foadi james_fo...@yahoo.co.uk: Dear all, (apologies for those being tired of similar questions...) I have tried using CAD on an unscaled MTZ from Mosflm. All I wanted to do was to change crystal name, dataset name and project name. This is what I got: - BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: CAD version 6.1 : 20/01/09## ### User: unknown Run date: 9/ 4/2009 Run time: 16:20:40 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B Data line--- TITLE Changing crystal, dataset and project names Data line--- LABIN FILE_NUMBER 1 ALL Data line--- DPNAME FILE_NUMBER 1 New New NONISO Data line--- DRENAME FILE_NUMBER 1 New New Insulin_01 Dataset_01 Data line--- END No CTYP lines input for file: 1 Indices output even if all data items flagged missing Warning, NOT all LABOUT data lines given OPENED INPUT MTZ FILE Logical Name: HKLIN1 Filename: exp_01/in1_MS_1_001.mtz * Title: Untitled * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 New New New 81.6000 81.6000 33.6000 90. 90. 120. 0.92000 * Number of Columns = 18 * Number of Reflections = 40898 * Missing value set to NaN in input mtz file * Number of Batches = 100 * Column Labels : H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS * Column Types : H H H Y B J Q J Q R R R R R R I I R * Associated datasets : 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 81.6000 81.6000 33.6000 90. 90. 120. * Resolution Range : 0.00109 0.32315 ( 30.345 - 1.759 A ) * Sort Order : 0 0 0 0 0 * Space group = 'H3' (number 146) File 1 is a multi-record MTZ file. Inputting a multi-record file to CAD is an unmitigated disaster! Please use MTZUTILS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- CAD: Input file is unmerged MTZ file. CAD: Input file is unmerged MTZ file. Times: User: 0.1s System: 0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B -- So it would appear that CAD is no good for this sort of files. What should I use, then? I have tried looking into mtzutils, but I don't see how to do it. Anyone for help? J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk web page:
Re: [ccp4bb] CAD on multi-record file
Don't use CAD. Use REBATCH. -James Holton MAD Scientist James Foadi wrote: Dear all, (apologies for those being tired of similar questions...) I have tried using CAD on an unscaled MTZ from Mosflm. All I wanted to do was to change crystal name, dataset name and project name. This is what I got: - BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: CAD version 6.1 : 20/01/09## ### User: unknown Run date: 9/ 4/2009 Run time: 16:20:40 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B Data line--- TITLE Changing crystal, dataset and project names Data line--- LABIN FILE_NUMBER 1 ALL Data line--- DPNAME FILE_NUMBER 1 New New NONISO Data line--- DRENAME FILE_NUMBER 1 New New Insulin_01 Dataset_01 Data line--- END No CTYP lines input for file: 1 Indices output even if all data items flagged missing Warning, NOT all LABOUT data lines given OPENED INPUT MTZ FILE Logical Name: HKLIN1 Filename: exp_01/in1_MS_1_001.mtz * Title: Untitled * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 New New New 81.6000 81.6000 33.6000 90. 90. 120. 0.92000 * Number of Columns = 18 * Number of Reflections = 40898 * Missing value set to NaN in input mtz file * Number of Batches = 100 * Column Labels : H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS * Column Types : H H H Y B J Q J Q R R R R R R I I R * Associated datasets : 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 81.6000 81.6000 33.6000 90. 90. 120. * Resolution Range : 0.001090.32315 ( 30.345 - 1.759 A ) * Sort Order : 0 0 0 0 0 * Space group = 'H3' (number 146) File 1 is a multi-record MTZ file. Inputting a multi-record file to CAD is an unmitigated disaster! Please use MTZUTILS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- CAD: Input file is unmerged MTZ file. CAD: Input file is unmerged MTZ file. Times: User: 0.1s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B -- So it would appear that CAD is no good for this sort of files. What should I use, then? I have tried looking into mtzutils, but I don't see how to do it. Anyone for help? J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk web page:
Re: [ccp4bb] CAD on multi-record file
or Pointless On 9 Apr 2009, at 18:09, James Holton wrote: Don't use CAD. Use REBATCH. -James Holton MAD Scientist James Foadi wrote: Dear all, (apologies for those being tired of similar questions...) I have tried using CAD on an unscaled MTZ from Mosflm. All I wanted to do was to change crystal name, dataset name and project name. This is what I got: - BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: CAD version 6.1 : 20/01/09## ### User: unknown Run date: 9/ 4/2009 Run time: 16:20:40 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B Data line--- TITLE Changing crystal, dataset and project names Data line--- LABIN FILE_NUMBER 1 ALL Data line--- DPNAME FILE_NUMBER 1 New New NONISO Data line--- DRENAME FILE_NUMBER 1 New New Insulin_01 Dataset_01 Data line--- END No CTYP lines input for file: 1 Indices output even if all data items flagged missing Warning, NOT all LABOUT data lines given OPENED INPUT MTZ FILE Logical Name: HKLIN1 Filename: exp_01/ in1_MS_1_001.mtz * Title: Untitled * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 New New New 81.6000 81.6000 33.6000 90. 90. 120. 0.92000 * Number of Columns = 18 * Number of Reflections = 40898 * Missing value set to NaN in input mtz file * Number of Batches = 100 * Column Labels : H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART FLAG BGPKRATIOS * Column Types : H H H Y B J Q J Q R R R R R R I I R * Associated datasets : 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 81.6000 81.6000 33.6000 90. 90. 120. * Resolution Range : 0.001090.32315 ( 30.345 - 1.759 A ) * Sort Order : 0 0 0 0 0 * Space group = 'H3' (number 146) File 1 is a multi-record MTZ file. Inputting a multi-record file to CAD is an unmitigated disaster! Please use MTZUTILS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- CAD: Input file is unmerged MTZ file. CAD: Input file is unmerged MTZ file. Times: User: 0.1s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B -- So it would appear that CAD is no good for this sort of files. What should I use, then? I have tried looking into mtzutils, but I don't see how to do it. Anyone for help? J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk web page:
Re: [ccp4bb] CAD on multi-record file
Many thanks for all your answers! It appears that using REBATCH is the best option for me, as I'm not planning on using SCALA (or POINTLESS) on this unmerged file. Keywords were as follows (for those who might be interested): TITLE Change Project, crystals and datasets name_ change batch numbers BATCH 1 TO 100 PNAME NONISO XNAME Insulin_01 DNAME Dataset_01 END Best wishes, J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk
