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: [log in to unmask]
> Subject: Re: [ccp4bb] Bug in c_truncate?
> To: [log in to unmask]
>
> 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, [log in to unmask] 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:[log in to unmask]] On Behalf Of
> > George M. Sheldrick
> > Sent: Friday, October 29, 2010 12:30 PM
> > To: [log in to unmask]
> > 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: [log in to unmask]
> >>>> Subject: Re: [ccp4bb] Bug in c_truncate?
> >>>> To: [log in to unmask]
> >>>>
> >>>> 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
> >>
> >>
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