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Hi Ed, The behavior you attribute to early versions of scalepack is still described in the current manual. See the section on "unit cell" (on p. 139 (printed) or p .140 of the pdf file - http://www.hkl-xray.com/hkl_web1/hkl/manual_online.pdf ). The manual states that the default value is taken from the value in the first header encountered unless you give it the UNIT CELL keyword. It also warns that "the postrefined value of the unit cell constants is not used nor is it output in the Scalepack output file. You must get this information from the log file if you are interested in it." The hkl web-site states that this version of the manual "(Edition 6, September 2003) corresponds to version 1.97 of the HKL program suite. Most commands from previous program versions work on the same way as in present version. " I think this still holds true for this command as well. (At least this is the case with a recent scalepack run using "HKL data processing system Version 1.98.2".) So you may need to go back to inserting cell parameters in your scalepack2mtz command files. Regards, Mitch -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Edward Berry Sent: Monday, January 09, 2006 2:37 PM To: Alessio Accardi Cc: [email protected] Subject: Re: [ccp4bb]: Unit Cell Parameters *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** If I understand correctly, the values from the log-file are the post-refined cell parameters, these are what you should use. In early versions of scalepack, the cell parameters at the top of the scalepack output (".sca") file seemed to be taken from the very first denzo (".x") file read, and were sometimes quite inaccurate. I had the impression that the last several versions, 1.79.9 at least, have corrected this and now the postrefined values are put at the top of the output file. Someone correct me if I am wrong, because in that case I need to go back to inserting cell param in the scalepack2mtz com file. Ed Alessio Accardi wrote: > Hi all, > > I am very sorry if I have a somewhat trivial question, but I am quite > new to the crystallography world. > I process my data with Denzo followed by Scalepack and I noticed that > the unit cell parameters in the scalepack .log file and in the final > output *.sca file are different; not by much, at most around 1-1.5%. > > This is the readout from the middle of the scalepack.log file: > > Hkl's refined: 379123 N.Chi**2: 1.227 Decrease: 0.000 * 379123 > = 0.5 > Film # a b c alpha beta gamma crysz > crysy crysx mosaicity > 1 232.332 97.983 170.963 90.000 131.210 90.000 75.087 > 18.917 135.045 1.082 > 2 232.332 97.983 170.963 90.000 131.210 90.000 75.126 > 18.942 135.056 1.082 > 3 232.332 97.983 170.963 90.000 131.210 90.000 75.124 > 18.933 135.057 1.082 > 4 232.332 97.983 170.963 90.000 131.210 90.000 75.126 > 18.930 135.056 1.082 > 5 232.332 97.983 170.963 90.000 131.210 90.000 75.117 > 18.908 135.052 1.082 > > And this is the readout from the top of the output.sca file: > > 230.822 97.684 170.202 90.000 131.114 90.000 c2 > > First of all which of the two sets of values is the correct one to use > in refinement? I would guess that the right one is the one in the .sca > file as the hkl's and intensities refer to that unit cell, but I am not > sure. Also, why are the values different? do they reflect different > stages of refinement of the processed data? if so, is the one in the > .sca file the more refined one? > > > Thank you > > Alessio > Brandeis University > > >
