Tim, Although I always like to advocate XPREP, that would not work because the .sca format - most unfortunately - does not know about free R flags.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 29 Oct 2010, Tim Gruene wrote: > Hello Peter, > > the easiest way to overcome the problem might be to use xprep to export to > sca-format and use scalepack2mtz for the conversion. That seems to be the > least > hasslesome way, although I am not totally sure that this procedure preserves > the > R-free flags set by xprep. > > Tim > > On Thu, Oct 28, 2010 at 12:48:14PM -0400, Peter Chan wrote: > > > > Hello Tim, > > > > Thank you for the suggestion. I have now tagged the working set as "1" and > > test set as "0". Unfortunately, it still gives the same error about all > > Rfree being the same, and only in c-truncate but not old-truncate. Perhaps > > I should install 6.1.3 and see if the problem still persist. > > > > Best, > > Peter > > > > > Date: Thu, 28 Oct 2010 16:29:31 +0200 > > > From: t...@shelx.uni-ac.gwdg.de > > > Subject: Re: [ccp4bb] Bug in c_truncate? > > > To: CCP4BB@JISCMAIL.AC.UK > > > > > > Hello Peter, > > > > > > I faintly rememeber a similar kind of problem, and think that if you > > > replace > > > "-1" with "0", the problem should go away. It seemed that "-1" is not an > > > allowed > > > flag for (some) ccp4 programs. > > > > > > Please let us know if this resolves the issue. > > > > > > Tim > > > > > > On Thu, Oct 28, 2010 at 10:21:20AM -0400, Peter Chan wrote: > > > > > > > > > > > > > > > > > > > > Dear Crystallographers, > > > > > > > > Thank you all for the emails. Below are some details of the procedures > > > > I performed leading up to the problem. > > > > > > > > The reflection file is my own data, processed in XDS and then flagging > > > > FreeR's in XPREP in thin resolution shells. I am using CCP4i version > > > > 6.1.2. I tried looking for known/resolved issues/updates in version > > > > 6.1.3 but could not find any so I assumed it is the same version of > > > > f2mtz/ctruncate/uniqueify. > > > > > > > > > > > > I used the GUI version of F2MTZ, with the settings below: > > > > > > > > - import file in SHELX format > > > > > > > > - "keep existing FreeR flags" > > > > > > > > - fortran format (3F4.0,2F8.3,F4.0) > > > > > > > > - added data label "I other integer" // FreeRflag > > > > > > > > The hkl file, in SHELX format, output by XPREP look something like this: > > > > > > > > -26 -3 1 777.48 39.19 > > > > 26 -3 -1 800.83 36.31 > > > > -26 3 -1 782.67 37.97 > > > > 27 -3 1 45.722 25.711 -1 > > > > -27 3 1 -14.20 31.69 -1 > > > > > > > > Notice the test set is flagged "-1" and the working set is not flagged > > > > at all. This actually lead to another error message in f2mtz about > > > > missing FreeR flags. From my understanding, the SHELX flagging > > > > convention is "1" for working and "-1" for test. So I manually tagged > > > > the working set with "1" using vi: > > > > > > > > -26 -3 1 777.48 39.19 1 > > > > 26 -3 -1 800.83 36.31 1 > > > > -26 3 -1 782.67 37.97 1 > > > > 27 -3 1 45.722 25.711 -1 > > > > -27 3 1 -14.20 31.69 -1 > > > > > > > > This is the file which gives me the error message: "Problem with FREE > > > > column in input file. All flags apparently identical. Check input > > > > file.". Apparently, import to mtz works ok when I use old-truncate > > > > instead of c-truncate. > > > > > > > > Best, > > > > Peter > > > > > > > -- > > > -- > > > Tim Gruene > > > Institut fuer anorganische Chemie > > > Tammannstr. 4 > > > D-37077 Goettingen > > > > > > phone: +49 (0)551 39 22149 > > > > > > GPG Key ID = A46BEE1A > > > > > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A > >
