Hi Graeme,the easiest way (which you did not mention) to obtain a .mtz file from XDS is of course to use XDSCONV with CCP4 as filetype. XDSCONV then writes a sequence of shell commands (essentially running f2mtz) to the screen which you just copy and paste to obtain a .mtz file (without R_free flag).
Depending on whether you specify FRIEDEL'S_LAW=FALSE or FRIEDEL'S_LAW=TRUEin XDSCONV.INP the resulting .mtz file (in addition to FP and SIGFP) will have DANO and SIGDANO, or not.
Of course, one does not get the statistics from TRUNCATE in this way.
HTH, Kay Winter, G (Graeme) wrote:
*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hi Mario, DANO and SIGDANO are written by truncate - are you running truncate as part of the scaling? Also - I presume you have selected the "separate anomalous pairs" check box... In terms of getting the data from XDS you may be better off using XDSCONV and specifying IALL as the file type - this will (after following the provided f2mtz script) give you an MTZ file. Make sure you have set FREIDEL'S_LAW=FALSE though all the way through XDS. A final option is to take the scaled but unmerged reflections from XSCALE, feed them through combat and merge them with Scala. This is nice because it provides CCP4 loggraph output you can analyse as usual, though does involve more work with scripts like: (SCALED.HKL is the output from XSCALE) #!/bin/bash combat hklin SCALED.HKL hklout SCALED.HKL.tmp1 << eof scale 0.02 input XDSASCII pname default dname xds eof sortmtz hklin SCALED.HKL.tmp1 hklout scaled_scala.mtz.tmp2 << eof H K L M/ISYM BATCH eof scala hklin scaled_scala.mtz.tmp2 hklout scaled_scala.mtz << eof run 1 all scales constant initial unity anomalous on eof Hope this helps... Cheers, Graeme -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mario Sanches Sent: 24 May 2006 02:23 To: [email protected] Subject: [ccp4bb]: pirate expiration (solved) and DANO column zeroed problem *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***Thank you for the tip Martyn. It turned out that I was running an old version of pirate which was installed with ccp4 5.99.Unfortunately I have another problem (not related to pirate, though): When I run SCALA after processing a dataset with MOSFLM I see that the DANO and SIGDANO column are all zeroed, even though I specified that thedataset have anomalous signal (that signal was clear on the statistics generated by SCALA).When I try to convert data from the same dataset processed with XDS (shelx format) to mtz using IMPORT I realized that the problem was on f2mtz, which writes only I and SIGI instead of I(+) and I(-) so that allthe following programs did not have access to the anomalous difference.I reinstalled CCP4 to try to fix this problem, but it persisted. Does anyone knows how to fix it?Thank you very much, Mario Sanches Martyn Winn wrote:I'm pretty sure this text doesn't exist in the CCP4 6.0 version of pirate.I would suspect you are picking up a different version by accident. Can you do "which cpirate" from the command line? Cheers Martyn On Mon, 22 May 2006, Mario Sanches wrote:*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** I am trying to run pirate and it fails with the following message: This program has expired: download a new versionI am running it under CCP4 6.0.0 on linux (kubuntu). Since this is a newversion of ccp4 I thought the problem could be something else otherthanexpiration of the program. Anyway, I don't knwo where to get a new version of pirate, if that is really the problem. Any help?Thank you in advance, Mario Sanches***************************************************************************** Dr. Martyn Winn**** Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND** Tel: +44 1925 603455 E-mail: [EMAIL PROTECTED] (personal)** Fax: +44 1925 603825 E-mail: [EMAIL PROTECTED] (CCP4 problems)** URL: http://www.ccp4.ac.uk/martyn/martyn.html************************************************************************ ***
-- Kay Diederichs http://strucbio.biologie.uni-konstanz.de/~kay email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz
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