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CCP4BB  August 2018

CCP4BB August 2018

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Subject:

Re: cell discrepancies and stuck refinement using different XDS-versions

From:

Kay Diederichs <[log in to unmask]>

Reply-To:

Kay Diederichs <[log in to unmask]>

Date:

Tue, 7 Aug 2018 20:49:09 +0200

Content-Type:

text/plain

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Parts/Attachments

text/plain (139 lines)

Dear all,
I post this again to CCP4BB because some people informed me that they 
received an empty email from me. This time I use my email client; 
previously I used the Jiscmail web interface - does anybody know what 
went wrong? Hopefully it works this time. Sorry if you get this twice.
Kay

Dear Sabine,

indeed, the differences between the last XDS versions are in the area of 
indexing, with  BUILT=20180409 being the most robust (and recommended) 
one. This gives the desired results in all my tests, and GlobalPhasing 
has successfully tested it with ~60 difficult cases. But there is no 
rule without exception, which means that it could nevertheless give the 
wrong answer in your case.

According to CCP4 othercell, the two cells that you cite are related by 
the [h-2l,-h,k] reindexing operator. However the cell volumes differ by 
slightly more than a factor of 2 , namely 232274 / 110672 = 2.1 which I 
find astonishing because typically such different indexing results 
result in a pseudo-centering situation, where the indexing results 
differ in that one tries to explain the weak and strong reflections, 
whereas the other only explains the strong reflections. What exactly 
happens in your case I don't know; I'd have to see the data and the 
detailed output of XDS. It could also be a case of two lattices (from 
two crystals) superimposed.

You can probably get the small cell with  BUILT=20180409 if you either
a) specify it in XDS.INP (together with SPACE_GROUP_NUMBER=1)
b) or remove the weak reflections from SPOT.XDS
c) or by adjusting some parameters in XDS.INP

To really understand what is going on in your case, you could
a) run the checkcentering program (from 
ftp://turn5.biologie.uni-konstanz.de/pub/linux_bin ) which will analyze 
your data w.r.t. pseudo-centering (similar to what pointless does)
b) look, in a representation of reciprocal space, at the spots that are 
used for indexing and that are indexed, or not. For this, you need the 
spot2pdb program (same download directory). Run it
grep -s allow-duplicate-sequence-numbers ~/.coot || echo 
"(allow-duplicate-sequence-numbers)" >>~/.coot
spot2pdb
coot SPOT-*.pdb
as suggested in 
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSGUI#tools

BTW it is normal that R factors with tNCS are higher ("stuck") than 
without; this is due to the wider distribution of reflection intensities 
in the case of tNCS (many weak ones, and many strong ones; less with 
intermediate intensity). Most people would say that the space group and 
cell where the refinement proceeds best must be the correct one; however 
if that does not explain all the reflections of the lattice then this is 
not quite satisfactory.

best wishes,

Kay


On Mon, 6 Aug 2018 16:50:56 +0200, Sabine Schneider 
<[log in to unmask]> wrote:

 >Dear all,
 >
 >We are encountering a differences in indexing using different XDS
 >versions, which results in either 2 or 4 mols/asu (SG P1; structure
 >determination via MR (30% seq ID model)) and either successful
 >refinement or stuck R/Rfree
 >
 >- the data were collected at ESRF ID30A3 (Aiger detector) and extend to
 >about 2.3A resolution (CC1/2 ~50%)
 >
 >The XDS version build 20180126 (and or autoprocessing at the ESRF via
 >autoproc, dials, xdsapp or grenade -> here also xds version from
 >20180126 used) gives us:
 >
 >P1  38.65    50.76    61.11 110.057  99.945  90.197
 >XDS complains and I need to use "DEFPIX INTEGRATE CORRECT"
 >-> 2mols/asu, structure refines to R/Rfree of 22/25
 >
 >In contrast the actual XDS-Version BUILT=20180409 results in:
 >P1  39.2   51.3  116.8  86.3  82.3  89.8
 >but XDS runs smoothly.
 >-> 4mols/asu, tNCS, R/Rfree stuck at 28/32
 >If I feed XDS with the smaller cell above, it fails.
 >
 >(The smaller cell is also found by Xia2/dials via the CCP4i2 interface.)
 >
 >Thus I am wondering, what are the differences between the two
 >XDS-versions? (I remember vaguely that there was a tread about different
 >XDS-versions, but couldn't find it..)
 >
 >Cheers Sabine
 >
 >
 >--
 >------------------------------------------
 >Dr. Sabine Schneider
 >Research Group Leader
 >Technical University of Munich
 >Department of Chemistry
 >Chair of Biochemistry
 >Lichtenbergstr. 4
 >85748 Garching
 >Germany
 >Tel.: +49 (0) 89 289 13759
 >Fax: +49 (0) 89 289 13363
 >http://www.biochemie.ch.tum.de/index.php?id=919
 >
 >--
 >------------------------------------------
 >Dr. Sabine Schneider
 >Research Group Leader
 >Technical University of Munich
 >Department of Chemistry
 >Chair of Biochemistry
 >Lichtenbergstr. 4
 >85748 Garching
 >Germany
 >Tel.: +49 (0) 89 289 13759
 >Fax: +49 (0) 89 289 13363
 >http://www.biochemie.ch.tum.de/index.php?id=919
 >
 >########################################################################
 >
 >To unsubscribe from the CCP4BB list, click the following link:
 >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
-- 
Kay Diederichs                http://strucbio.biologie.uni-konstanz.de
email: [log in to unmask]    Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universit├Ąt Konstanz, Box M647, D-78457 Konstanz

This e-mail is digitally signed. If your e-mail client does not have the
necessary capabilities, just ignore the attached signature "smime.p7s".

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