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CCP4BB  February 2010

CCP4BB February 2010

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Subject:

Re: HKL-MTZ conversion

From:

Frank von Delft <[log in to unmask]>

Reply-To:

Frank von Delft <[log in to unmask]>

Date:

Fri, 5 Feb 2010 12:23:13 +0000

Content-Type:

text/plain

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Parts/Attachments

text/plain (124 lines)

One thing that is superior is that the scala output gives you a better 
feel for the data quality, especially thanks to the per-image plots, for 
things like B-factor decay.

Or should I say:  it works better for *me*.  All other scaling programs 
are more terse than scala, but maybe I've just never figured out where 
to look.

phx.




On 05/02/2010 10:42, Phil Evans wrote:
> On 5 Feb 2010, at 10:35, George M. Sheldrick wrote:
>
>    
>> PROTEUM (and APEX) are the names Bruker uses to describe the instrument
>> control software; they write out frames in Bruker format. In the standard
>> Bruker system the frames are integrated by SAINT which outputs reflection
>> records in Bruker .raw format (not to be confused with a different .raw
>> format produced by Bruker powder systems). EVAL, XDS, d*TREK and possibly
>> other integration programs can also process Bruker frames, but only SAINT
>> and EVAL can currently integrate the diffraction patterns of
>> non-merohedrally twinned and modulated structures (in up to 6 dimensions).
>>
>> For scaling Bruker provides SADABS (for scaling normal and modulated
>> structures) and TWINABS (for non-merohedral twins). SADABS provides a
>> similar functionality to SCALEPACK and SCALA and outputs merged or
>> unmerged reflection lists in various ASCII formats that can be converted
>> to .mtz by e.g. the CCP4 program COMBAT. TWINABS writes SHELX HKLF 5
>> format .hkl files for refinement of non-merohedral twins with SHELXL and
>> can also produce 'detwinned' HKLF 4 format files that can be input to
>> CCP4 by COMBAT and then treated in the same way as data from untwinned
>> crystals.. These are better quality than conventional 'detwinned' data
>> because they use the SAINT partitioning of overlapping reflections, as
>> a 'restraint' in the 'refinement' of the unique reflection intensities
>> against the total intensities of the composite reflections (the
>> 'observations'. We have even used the resulting data successfully for
>> Sulfur-SAD phasing.
>>
>> I presume that the latest POINTLESS is reading the .raw files written by
>> SAINT. It would be rather useful if some impartial person could compare
>> the data quality obtained via the SAINT-POINTLESS-SCALA and
>> SAINT-SADABS-(XPREP)-COMBAT routes; anyone who is using SAINT will also
>> have SADABS and it only takes a few seconds to run.
>>
>>      
> Yes Pointless read .raw files, based on documentation for SAINT and some example files kindly supplied to me.
>
> I have no reason suppose that the POINTLESS-SCALA route is superior to any other, but it has been requested by users.
> I am also aware that in comparing different data processing routes it is very difficult to decide whether one route is "better" than another. What is the score?
>
> Note that earlier versions of Pointless&  Scala than the ones I mentioned here are wrong for Phi scans on a 3-axis goniostat (the geometry calculation for secondary absorption was wrong, I think because I originally assumed that people would always use Omega scans)
>
> Phil
>
>    
>> 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, 5 Feb 2010, Phil Evans wrote:
>>
>>      
>>> The latest latest version of Pointless from our ftp server here will convert output from SAINT to mtz for input into Scala etc. I'm guessing that Proteum X8 is the same as SAINT (is it?)
>>>
>>> Phil
>>>
>>>        
>>>>>>>                
>>> I've done some work on Pointless&  Scala to try to make them work properly for Saint Phi scans, and to allow for Phi going backwards. I believe I now have it working correctly (I hope)
>>>
>>> The files are on our ftp site
>>>
>>> ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/
>>>
>>> pointless-1.4.9.tar.gz     source
>>> pointless-1.4.9.linux      executable
>>>
>>> scala-3.3.18.tar.gz        source
>>> scala-3.3.18.linux         executable
>>>
>>>
>>> On 5 Feb 2010, at 06:36, Sylvia Fanucchi wrote:
>>>
>>>        
>>>> Use combat
>>>>
>>>> -----Original Message-----
>>>> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>>>> Dr. STEPHEN SIN-YIN, CHUI
>>>> Sent: Friday, February 05, 2010 8:32 AM
>>>> To: [log in to unmask]
>>>> Subject: [ccp4bb] HKL-MTZ conversion
>>>>
>>>> Dear All,
>>>>
>>>> can anyone of you using Bruker PROTEUM X8? How can I convert HKL to MTZ
>>>> in
>>>> CCP4i?
>>>> I want to do data analysis (TRUNCATE) for the dataset.
>>>>
>>>> Many thanks!
>>>>
>>>> stephen
>>>>
>>>> -- 
>>>> Dr. Stephen Sin-Yin Chui
>>>> Research Assistant Professor,
>>>> Department of Chemistry,
>>>> The University of Hong Kong, Pokfulam Road,
>>>> Hong Kong SAR, China.
>>>> Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
>>>> <html><p><font face = "verdana" size = "0.8" color = "navy">This communication is intended for the addressee only. It is confidential. If you have received this communication in error, please notify us immediately and destroy the original message. You may not copy or disseminate this communication without the permission of the University. Only authorized signatories are competent to enter into agreements on behalf of the University and recipients are thus advised that the content of this message may not be legally binding on the University and may contain the personal views and opinions of the author, which are not necessarily the views and opinions of The University of the Witwatersrand, Johannesburg. All agreements between the University and outsiders are subject to South African Law unless the University agrees in writing to the contrary.</font></p></html>
>>>>          
>>>        

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