Hi Phil, I do, but the freeR flag problem is easily circumvented. One can just use cad with the output mtz from ctruncate and the input mtz:
cad \ HKLIN2 $WORKDIR/raw.mtz \ HKLIN1 $WORKDIR/ctruncate.mtz \ HKLOUT $WORKDIR/ctruncate_withRfree.mtz \ <<eof >>$WORKDIR/mtz_creation.log LABIN FILE 2 E1=FREE LABIN FILE 1 ALLIN END eof Cheers, Robbie ---------------------------------------- > Date: Fri, 29 Oct 2010 13:05:40 +0100 > From: p...@mrc-lmb.cam.ac.uk > Subject: Re: [ccp4bb] Bug in c_truncate? > To: CCP4BB@JISCMAIL.AC.UK > > The normal use of [c]truncate is to take intensities from Scala, so it > wouldn't expect FreeR flags in the file. > > I suppose this should be added for other uses of the program > > Is this something that is often used? Do people import intensities into CCP4 > to convert them to Fs? > > Phil > > > On 29 Oct 2010, at 13:01, herman.schreu...@sanofi-aventis.com wrote: > > > Dear Peter, > > > > Since I did not hear that your problem is solved here my two cents. I > > did some tests using the ccp4i option "Convert Intensities to SFs" and > > found that here ctruncate completely ignored the FreeRflags. So my > > conclusion is that ctruncate does not need FreeRflags and you can use > > the following procedure: > > > > 1) convert your hkl file (including FreeRflags) into an mtz with f2mtz > > without any special SHELX options. --> mtz 1 > > Careful: a FreeRflag of 1 means an unfree reflection and the free > > reflections have a FreeRflag of zero. > > 2) run ctruncate with the "Convert Intensities to SFs". You will loose > > your FreeRflags in this stage. --> mtz 2 > > 3) add the FreeRflags from mtz 1 to mtz 2 using cad. > > > > If you wish, I can give you a command file which will do this. It is a > > somewhat roundabout procedure and I hope that this bug (or feature) will > > be fixed by the next release of ccp4. > > > > Best, > > Herman > > > > -----Original Message----- > > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > > George M. Sheldrick > > Sent: Friday, October 29, 2010 12:30 PM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Bug in c_truncate? > > > > 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 > >> > >>
