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
