The way I do this is to use mtz2various which reads the SHELX output and
(I hope) copes with its various idiosymcrasies, producing an mtz file
with H k l I SigI FreeR
This can then be fed to the ctruncate GUI
You need - to request
Ensure unique data... Copy FreeR from another mtz file
Then the MTZin is the SHELX mtz conversion
and the MTZ with FreeR is the same file..
I think it works although I have no data to test it.
Eleanor
On 10/29/2010 01:05 PM, Phil Evans wrote:
> 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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