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CCP4BB  November 2012

CCP4BB November 2012

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Subject:

Re: Copying R-free flags - possibly daft question.

From:

Antony Oliver <[log in to unmask]>

Reply-To:

Antony Oliver <[log in to unmask]>

Date:

Mon, 5 Nov 2012 11:37:56 +0000

Content-Type:

text/plain

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Thanks Eleanor - guess I should have plumbed the depths of the CAD manual a little further.

Works perfectly.

Antony.

---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ

email: [log in to unmask]
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512

On Nov 5, 2012, at 11:24 AM, Eleanor Dodson wrote:

> Just give CAD the resolution cut off of the new data set..
> Eleanor
> From the CAD documentation..
> RESOLUTION [ RESOLUTION OVERALL <dmin> <dmax> ] | [RESOLUTION FILE_NUMBER <i> <dmin> <dmax> ]
> 
> Use either:
> 
> RESOLUTION OVERALL <dmin> <dmax>
> for overall resolution limits, or:
> RESOLUTION FILE_NUMBER <i> <dmin> <dmax>
> to set input limit for FILE_NUMBER <i>.
> <dmax>, <dmin> are the resolution limits for the data to be included, i.e. data are included for which 
> (1/<dmax>)**2 >= 4 sin**2theta/lambda**2 >=(1/<dmin>)**2 
> NOTE: Defaults are 0.1 and 1000.0 Angstrom.
> 
> 
> On 5 Nov 2012, at 09:53, Antony Oliver wrote:
> 
>> Am I worrying about something unnecessarily?
>> 
>> I have several protein-drug datasets, all in the same spacegroup, but wildly varying resolutions.
>> I wish to use the same reflections for calculating R-free in all cases.
>> 
>> Using xia2 with a reference dataset for both indexing and R-free seems to work fine, apart from the fact that the resulting mtz file, now contains R-free labels for reflections that have no observations… i.e. taken from the higher resolution "reference dataset"; see output below.
>> 
>> I get essentially the same results using CAD to copy the R-free column between mtzfiles….
>> 
>> Is this actually a problem - or is it just my innate sense of tidiness that wants the resolution values to be the same?
>> 
>> 
>> Many thanks,
>> 
>> Antony.
>> 
>>  Col Sort    Min    Max    Num      %     Mean     Mean   Resolution   Type Column
>>  num order               Missing complete          abs.   Low    High       label 
>> 
>>    1 ASC      0      36      0  100.00     14.2     14.2  57.66   2.02   H  H
>>    2 NONE     0      36      0  100.00     14.6     14.6  57.66   2.02   H  K
>>    3 NONE     0      38      0  100.00     14.8     14.8  57.66   2.02   H  L
>>    4 NONE    0.0    19.0   132   99.18     9.52     9.52  57.40   2.02   I  FreeR_flag
>>    5 NONE  -30.6 10855.5 11647   28.03   202.72   203.43  57.66   3.17   J  IMEAN
>>    6 NONE    1.5   356.4 11647   28.03    11.52    11.52  57.66   3.17   Q  SIGIMEAN
>>    7 NONE    7.8  1040.0 11647   28.03   109.05   109.05  57.66   3.17   F  F
>>    8 NONE    1.4    23.8 11647   28.03     6.59     6.59  57.66   3.17   Q  SIGF
>> 
>> 
>>  No. of reflections used in FILE STATISTICS    16183
>> 
>> 
>> 
>> 
>> 
>> ---
>> Dr Antony W Oliver
>> Senior Research Fellow
>> CR-UK DNA Repair Enzymes Group
>> Genome Damage and Stability Centre
>> Science Park Road
>> University of Sussex
>> Falmer, Brighton, BN1 9RQ
>> 
>> email: [log in to unmask]
>> tel (office): +44 (0)1273 678349
>> tel (lab): +44 (0)1273 677512
>> 
> 

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