Re: [ccp4bb] Wilson plot from truncated.mtz

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Research Associate position at the University of Missouri
From: Jack Tanner TannerJJ {- at -} MISSOURI {- dot -} EDU
Date: 2008-08-21

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Subject: Re: Wilson plot from truncated.mtz
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-08-21

Subject: Re: Wilson plot from truncated.mtz
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-08-21

Truncate output does by default contain I (aka F^2) columns
Phil

On 20 Aug 2008, at 20:25, George M. Sheldrick wrote:

> Ian,
>
> SHELXL users would also be very happy if mtz files routinely
> contained and its esd, but I had long regarded this as a
> lost cause.
>
> 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 Wed, 20 Aug 2008, Ian Tickle wrote:
>
>> Hi Jim
>>
>> You can just run Truncate again, exactly as you did before, but this
>> time using your truncated.mtz file as input, since it contains the
>> same
>> IMEAN/SIGIMEAN columns output by Scala. It will also give you
>> another
>> output mtz file which should be identical to your input mtz (but I
>> haven't tested this!). Truncate will also allow you to assign the
>> F/SIGF columns to get a Wilson plot (but no output mtz), but note
>> that
>> this is formally incorrect since squaring is not the same as
>> using
>> (i.e. = ^2 + var(F)).
>>
>> It seems to me that it would be better if in fact Truncate did
>> write out
>> a column (as well as ), because this should really be used
>> in
>> place of ^2 in Molecular Replacement, native Patterson, F^2 based
>> refinement, or indeed anywhere where F^2 is demanded (note that using
>> Imeas doesn't help because obviously it's not the same as
>> either).
>>
>> Cheers
>>
>> -- Ian
>>
>>> If I've lost my SCALA MTZ, and have only the truncated.mtz
>>> for my dataset, which program is the quickest means of
>>> obtaining a Wilson plot?
>>>
>>> Thank you again,
>>> Jim
>>>
>>>
>>> --- On Wed, 8/20/08, Eleanor Dodson wrote:
>>>
>>>> From: Eleanor Dodson
>>>> Subject: Re: [ccp4bb] Lower completeness, decent R factors,
>>> but low B factor...
>>>> To: CCP4BB@JISCMAIL.AC.UK
>>>> Date: Wednesday, August 20, 2008, 4:30 AM
>>>> James Pauff wrote:
>>>>> Hello all,
>>>>>
>>>>> I have a refined structure at 2.6 angstroms that at
>>>> about 73% completeness at this resolution. The I/sigma is
>>>> about 2.0 at 2.6 angstroms, and the omit density for my
>>>> ligands is great contoured at 3.0sigma. My Rcryst is 19 or
>>>> so and the Rfree is 24.5 or so.
>>>>>
>>>>> HOWEVER, my mean B value is 13.9, whereas my other 2
>>>> structures (at 2.2 and 2.3 angstroms, same protein, >95%
>>>> completeness) have mean B values of 22+. Any suggestions as
>>>> to what is going on here? I'm having trouble explaining
>>>> this.
>>>>>
>>>>> Thank you,
>>>>> Jim
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>> Have you used TLS - listed B factors will then be given
>>>> relative to the
>>>> TLS parameters. You need to run tLSANL to get a more
>>>> realistic value.
>>>> Eleanor
>>>>
>>>>
>>>> But in fact temperature factors are rather harder to
>>>> estimate at lower
>>>> resolutions than higher. Look at your and
>>>> curves v resolution
>>>> ( part of a REFMAC loggraph) and you can see that sometimes
>>>> the overall
>>>> scaling struggles to get a reasonable fit..
>>>
>>>
>>>
>>>
>>>
>>
>>
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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Research Associate position at the University of Missouri
From: Jack Tanner TannerJJ {- at -} MISSOURI {- dot -} EDU
Date: 2008-08-21

Next message:
Subject: Re: Wilson plot from truncated.mtz
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-08-21