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Revision as of 00:01, 28 February 2010

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post-webinar
(New page: These are answers to questions that were asked concerning XDS, on the occasion of the webinar on Feb 25, 2010. Some answers were given during the webinar; these are not repeated here. Q:...)
 
(post-webinar)
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These are answers to questions that were asked concerning XDS, on the occasion of the webinar on Feb 25, 2010. Some answers were given during the webinar; these are not repeated here.
These are answers to questions that were asked concerning XDS, on the occasion of the webinar on Feb 25, 2010. Some answers were given during the webinar; these are not repeated here.


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Q: Is there a way to automatically set the high resolution limit based on an I/sigma cutoff?
Q: Is there a way to automatically set the high resolution limit based on an I/sigma cutoff?
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A: no.
A: no.


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Q: How does one define the beam stop shadow?  Is it possible to develop a simple method, e.g. the ignore circle and ignore rectangle of HKL2000?
Q: How does one define the beam stop shadow?  Is it possible to develop a simple method, e.g. the ignore circle and ignore rectangle of HKL2000?
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A: VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= and UNTRUSTED_RECTANGLE= are the primary means. UNTRUSTED_CIRCLE may be implemented soon.
A: VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= and UNTRUSTED_RECTANGLE= are the primary means. UNTRUSTED_CIRCLE may be implemented soon.


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Q: Can one apply the corrections in CORRECT without deleting outliers (i.e. waiting for a later program e.g. SCALA to do outlier rejection).
Q: Can one apply the corrections in CORRECT without deleting outliers (i.e. waiting for a later program e.g. SCALA to do outlier rejection).
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A: you may set WFAC1 to 100 (default is 1)
A: you may set WFAC1 to 100 (default is 1)


 
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Q: What is LATTICE-CHARACTER in CORRECT.LP ?
Q: What is LATTICE-CHARACTER in CORRECT.LP ?
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A: the error should be less than half the minimum spot separation. XDS does optimize the beam position.
A: the error should be less than half the minimum spot separation. XDS does optimize the beam position.


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Q: I can not find generate_XDS.INP in XDSwiki page
Q: I can not find generate_XDS.INP in XDSwiki page
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A: try http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP
A: try http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP
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A: try http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_prepare.html
A: try http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_prepare.html


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A: Using XDS-Viewer: along the x direction, you find the "integration batches" (last frames on the right). Along the y direction, the resolution ranges. The shades of gray correspond to numbers - move the mouse across them. The numbers are scalefactors multiplied with 1000.
A: Using XDS-Viewer: along the x direction, you find the "integration batches" (last frames on the right). Along the y direction, the resolution ranges. The shades of gray correspond to numbers - move the mouse across them. The numbers are scalefactors multiplied with 1000.
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Q: What about overlapping reflections in XDS?
Q: What about overlapping reflections in XDS?
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A: yes, because the programs implement different ideas.  
A: yes, because the programs implement different ideas.  


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Q: Is there a way to automatically set the high resolution limit based on and I/sigma cutoff?
Q: Is there a way to automatically set the high resolution limit based on and I/sigma cutoff?
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A: no.
A: no.


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What about very low resolution data, 5 to 10 A range with the rather high mosaicity of few degrees? Any experience with processing of such data with the XDS?
A: yes, I have lots of experience with bad data. It should be possible to process these data. You may want to specify
BEAM_DIVERGENCE=  BEAM_DIVERGENCE_E.S.D.=
REFLECTING_RANGE=  REFLECTING_RANGE_E.S.D.=
in XDS.INP, and to use REFINE(INTEGRATE)=


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Q: You said that the XDS deals with high mosaicity. How high mosaicity is still manageable?


Colin Levy What is the best way to deal with weak data with a long cell axis (ie. very close spots)
A: I don't have exact numbers. Maybe up to ten degrees?


Alice Douangamath Have been told that XDS does not deal well with ice rings. Is it true? What is the problem there? What other way beside excluding the ice rings?
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Nick Sennett How do you interpret the DECAY.cbf file?
Q: Could you give recommendation for MAD data processing, to get best anomalous??
How to process the 3 data sets with the same orientation matrix, should we use
reference datataset?


A: First question: see XDSwiki. Second question: yes.


Alejandro Buschiazzo There are ‘several’ R-factor figurest in the logs: could you comment on their
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differences/advantages?


Aleksander Roszak What about very low resolution data, 5 to 10 A range with the rather high mosaicity of few degrees? Any experience with processing of such data with the XDS?
Q: It would be nice to have a Table with Rfactors for each Image to identify xtal damage.
I meant Table with Ractor over Image in CORRECT.LP


You said that the XDS deals with high mosaicity. How high mosaicity is still manageable?
A: XDSSTAT produces this table.


Roberto Steiner What is the best way in XDS to understand whether particular frames should be
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rejected? Is there an Rmerge/frame table in CORRECT.LP?
Q: Is it possible to exclude images inside the frame range from integration?


Jose Casasnovas Could you give recommendation for MAD data processing, to get best anomalous??
A: just remove them from the directory, or change their name. Or create a directory with symlinks only to those file you want XDS to use.
How to process the 3 data sets with the same orientation matrix, should we use  
reference datataset?


It would be nice to have a Table with Rfactors for each Image to identify xtal damage.
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I meant Table with Ractor over Image in CORRECT.LP


Pius Padayatti how well XDS will handle weakly diffracting images?especially highly mosaic patterns, is there
Q: how to identify whether the data processed had a good anomalous signal?
an option to play with mosaicity etc like in the case of HKL?


A: look at anomalous correlation: if it is > 90% at low resolution it is definitely good.


Loannis Manolaridis Thank you for the very useful seminar.
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Bartholomeus Kuettner Is it possible to exclude images inside the frame range from integration?


Lirong Chen how to identify whether the data processed had a good anomalous signal?
Q: All my crystals are split, and HKL200 has a hard time indexing the unit cell using sequential  
 
Donal Raymond All my crystals are split, and HKL200 has a hard time indexing the unit cell using sequential  
frames. However, iMOSFLM does a really good job indexing using orthagonal frames. Can XDS  
frames. However, iMOSFLM does a really good job indexing using orthagonal frames. Can XDS  
index the unit cell using orthagonal frames?
index the unit cell using orthagonal frames?


Ulrich Englich What is the best way to vreate mtz files? With the Xscale/xdsconv I often obtain intensity values
A: yes. You can define several SPOT_RANGE= keyword/parameter pairs, e.g. SPOT_RANGE=1 1 SPOT_RANGE=90 90 .
that are marked *** stars - probably overshooting a formatting limit.


Xiaoyun Ji Which command lines should be refered to when dealing with really weak data?
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Is there a way if the diffraction is kind of multple latticed? I mean when the automatic procedure
Q: What is the best way to create mtz files? With the Xscale/xdsconv I often obtain intensity values that are marked *** stars - probably overshooting a formatting limit.
failed due to the weak diffraction.


Nikolina Sekulic I wold like to be added to e-mail list on when slides will be available
A: do you mean the *** stars appear in the output of mtzdump? That would be a problem of mtzdump only, and irrelevant for the use of the MTZ file. The XDS/XSCALE/XDSCONV route should not produce these stars (the proper Fortran formats are used throughout).


When evaluating the processing results in CORRECT.LP, what should be done if chi2is is far
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fom 1.0 ? Is there any help to that?


Jonathan Grimes How does one check youve got the ice-rings excluded correctly ? (ie Is there a visual way of  
Q: How does one check you've got the ice-rings excluded correctly ? (ie Is there a visual way of  
checking?)
checking?)


Lynn Gregory-Pauron Which Rfactor do you use for publishing the structure? Do I use the Rmeas at -3 sigma (from
A: look at the Wilson plot.
XSCALE.LP), and why?
 
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Q: The background range is defined as first 5 degrees by default. Is this an assumption that the background (used in Integrate?) remains consistent over the entire dataset valid? The spots over the entire dataset still have background corrected based on first 5 degrees?


Karthik Sathiyamoorthy The background range is defined as first 5 degrees by default. Is this an assumption that the  
A: No. The INIT step uses the first 5 degrees (by default) for a number of purposes (check out the files written by INIT !). BKGINIT.cbf is essentially used only for scaling purposes; the ''real'' background calculation just requires the frame which has the reflections whose background.
background (used in Integrate?)remains consistent over the entire dataset valid? The spots
over the entire dataset still have background corrected based on first 5 degrees?
Kay
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