Re: [ccp4bb] scale data with multiple MTZ files
There is an (possibly) easier way now in pre-release 1) Download install (manually) from the CCP4 pre-release site the program pointless and the ccp4i task interface 2) Use the Find or Match Laue Group option (under Data Reduction) to open the interface window to the program Pointless This will allow input of multiple MTZ files (or indeed files from XDS Scalepack), check them for consistent indexing if appropriate, and enforce unique batch numbers (a long-standing irritation). By default it will try to determine the Laue group space group, but it can also match space group indexing with a reference file, or just sort the files together (replacing sortmtz). 3) Put the output (HKLOUT) file into Scala (Scale and Merge intensities task) Note that Pointless ( Scala) are still (!) under development, and the versions in the next CCP4 release (or indeed pre-release) will be updates of these versions. Latest versions of Pointless Scala are also available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/ Phil On 11 Jan 2008, at 05:40, Roger Rowlett wrote: Huiying Li wrote: I tried to scale, using SCALA through CCP4i GUI, three blocks of data collected with one crystal (3 mtz files output from MOSFLM). The GUI has only one MTZ input slot. Which program can be used to combine the 3 unmerged mtz files together? CAD refused to handle these raw mtz files. Thanks in advance for any help. Huiying Using the CCP4 GUI, employ the following steps: 1. Open a Sort/Modify/Combine job and renumber your data sets (reset batch numbers option). A simple method is to add 1000 to the batch numbers for one data set and 2000 to the batch numbers for the second data set (assuming you have less than 999 frames of data output from MOSFLM.) 2. Open another Sort/Modify/Combine job and combine the renumbered MTZ files into one merged file. Click on Add File to add additional renumbered batches from step 1. Each batch of reflections will now have unique batch numbers. 3. Open a Scale and Merge Intensities task window. Select as your input the sorted and combined file output from step 2. In the Define Datasets section, choose Combine All Input Datasets into a Single Output Dataset. You can convert the scaled intensities to structure factors by checking the appropriate box. The combined datasets will not have monotonically varying R(merge) values across batches (1-1000, 1001-2000, 2001-3000) becuase of discontinuities in the data. However the merged datasets should have good overall statistics if appropriate for merging. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
Re: [ccp4bb] scale data with multiple MTZ files
Hi There's a way to avoid having to do this - use the ADD sub-keyword when processing in Mosflm, so that the batch number for each image data is given an offset; see http://www.mrc-lmb.cam.ac.uk/harry/cgi-bin/keyword2.cgi?PROCESS Both the traditional X11 gui and the new iMosflm allow you to add an offset easily, allowing the subsequent CCP4 programs to work with multiple MTZ files produced by Mosflm. On 11 Jan 2008, at 09:49, Phil Evans wrote: There is an (possibly) easier way now in pre-release 1) Download install (manually) from the CCP4 pre-release site the program pointless and the ccp4i task interface 2) Use the Find or Match Laue Group option (under Data Reduction) to open the interface window to the program Pointless This will allow input of multiple MTZ files (or indeed files from XDS Scalepack), check them for consistent indexing if appropriate, and enforce unique batch numbers (a long-standing irritation). By default it will try to determine the Laue group space group, but it can also match space group indexing with a reference file, or just sort the files together (replacing sortmtz). 3) Put the output (HKLOUT) file into Scala (Scale and Merge intensities task) Note that Pointless ( Scala) are still (!) under development, and the versions in the next CCP4 release (or indeed pre-release) will be updates of these versions. Latest versions of Pointless Scala are also available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/ Phil On 11 Jan 2008, at 05:40, Roger Rowlett wrote: Huiying Li wrote: I tried to scale, using SCALA through CCP4i GUI, three blocks of data collected with one crystal (3 mtz files output from MOSFLM). The GUI has only one MTZ input slot. Which program can be used to combine the 3 unmerged mtz files together? CAD refused to handle these raw mtz files. Thanks in advance for any help. Huiying Using the CCP4 GUI, employ the following steps: 1. Open a Sort/Modify/Combine job and renumber your data sets (reset batch numbers option). A simple method is to add 1000 to the batch numbers for one data set and 2000 to the batch numbers for the second data set (assuming you have less than 999 frames of data output from MOSFLM.) 2. Open another Sort/Modify/Combine job and combine the renumbered MTZ files into one merged file. Click on Add File to add additional renumbered batches from step 1. Each batch of reflections will now have unique batch numbers. 3. Open a Scale and Merge Intensities task window. Select as your input the sorted and combined file output from step 2. In the Define Datasets section, choose Combine All Input Datasets into a Single Output Dataset. You can convert the scaled intensities to structure factors by checking the appropriate box. The combined datasets will not have monotonically varying R(merge) values across batches (1-1000, 1001-2000, 2001-3000) becuase of discontinuities in the data. However the merged datasets should have good overall statistics if appropriate for merging. Cheers, -- - --- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] scale data with multiple MTZ files
pointless now does this Phil On 11 Jan 2008, at 11:05, Frank von Delft wrote: There's a way to avoid having to do this - use the ADD sub- keyword when processing in Mosflm, so that the batch number for each image data is given an offset; see Nevertheless, it *is* a right-royal pain in the arse: you're cruising at the synchrotron, crystal collecting and quietly (or noisily) dying, you want a quick scale to know whether you have enough data from your second batch and scala craps at you for having the repeating batch number. Can't the merging process (pointless; sortmtz) be made to spot that batch numbers are repeating, and do an automatic add based on filename? After all, batches from the same range *always* end up in the same unmerged mtz file (or files with the same template). At least, I was able to write a csh script to do it, and if you can do it in csh, you can do it in anything... :) phx.
Re: [ccp4bb] scale data with multiple MTZ files
There's a way to avoid having to do this - use the ADD sub-keyword when processing in Mosflm, so that the batch number for each image data is given an offset; see Nevertheless, it *is* a right-royal pain in the arse: you're cruising at the synchrotron, crystal collecting and quietly (or noisily) dying, you want a quick scale to know whether you have enough data from your second batch and scala craps at you for having the repeating batch number. Can't the merging process (pointless; sortmtz) be made to spot that batch numbers are repeating, and do an automatic add based on filename? After all, batches from the same range *always* end up in the same unmerged mtz file (or files with the same template). At least, I was able to write a csh script to do it, and if you can do it in csh, you can do it in anything... :) phx.
Re: [ccp4bb] scale data with multiple MTZ files
The task - Sort/ Modify / Combine files does just that.. Eleanor Huiying Li wrote: I tried to scale, using SCALA through CCP4i GUI, three blocks of data collected with one crystal (3 mtz files output from MOSFLM). The GUI has only one MTZ input slot. Which program can be used to combine the 3 unmerged mtz files together? CAD refused to handle these raw mtz files. Thanks in advance for any help. Huiying
[ccp4bb] scale data with multiple MTZ files
I tried to scale, using SCALA through CCP4i GUI, three blocks of data collected with one crystal (3 mtz files output from MOSFLM). The GUI has only one MTZ input slot. Which program can be used to combine the 3 unmerged mtz files together? CAD refused to handle these raw mtz files. Thanks in advance for any help. Huiying -- Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: [EMAIL PROTECTED]
Re: [ccp4bb] scale data with multiple MTZ files
Huiying Li wrote: I tried to scale, using SCALA through CCP4i GUI, three blocks of data collected with one crystal (3 mtz files output from MOSFLM). The GUI has only one MTZ input slot. Which program can be used to combine the 3 unmerged mtz files together? CAD refused to handle these raw mtz files. Thanks in advance for any help. Huiying Using the CCP4 GUI, employ the following steps: 1. Open a Sort/Modify/Combine job and renumber your data sets (reset batch numbers option). A simple method is to add 1000 to the batch numbers for one data set and 2000 to the batch numbers for the second data set (assuming you have less than 999 frames of data output from MOSFLM.) 2. Open another Sort/Modify/Combine job and combine the renumbered MTZ files into one merged file. Click on Add File to add additional renumbered batches from step 1. Each batch of reflections will now have unique batch numbers. 3. Open a Scale and Merge Intensities task window. Select as your input the sorted and combined file output from step 2. In the Define Datasets section, choose Combine All Input Datasets into a Single Output Dataset. You can convert the scaled intensities to structure factors by checking the appropriate box. The combined datasets will not have monotonically varying R(merge) values across batches (1-1000, 1001-2000, 2001-3000) becuase of discontinuities in the data. However the merged datasets should have good overall statistics if appropriate for merging. Cheers, -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
