Re: [phenixbb] Multivariate Z score L-test
Thank you so much. I'll try all the space groups and see what happens. Many thanks again, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 ----------------------------------------
Date: Fri, 29 Jun 2007 07:35:22 -0700 From: [email protected] To: [email protected] Subject: Re: [phenixbb] Multivariate Z score L-test
Hi Claudia,
This could indicate that tyour data is actually P 2 1 1, P 1 2 1 or P 1 1 2 or P 21 1 1, P 1 21 1, P 1 1 21. Try processing that data in those spacegroups and see if that makes any difference. You might end up havig to refine your structure in all spacegroups to find out which possibility is the best.
It could also indicate that the quality of your data is not very good, either due to suboptimal data processing or because of bad diffraction (or both).
HTH
Peter
2007/6/29, Claudia Scotti :
Dear List,
I'm only at my third structure (a scFv antibody fragment) and I'm disturbing about a dataset that is giving problems at the refinement stage: it gets stuck at about Rcryst= 0.36 and Rfree=0.44.
I've tried data processing with several softwares (Mosflm, XDS, Denzo) and the result is consistently P222, unit cell 69x79x90, 90, 90, 90. The data are anisotropic, with limits at 2.3 and 2.8 A. I cut the data at 3.0 A. Matthews coefficient suggests two molecules per asu. No NCS is detected by self-rotation and a native Patterson detects a small peak (10% of origin peak) at 0.19, 0.34, 0.5. MR using several softwares (AmoRe, Molrep and Phaser) and several models all agree that the best space group is P21212, though the systematic absences are not perfectly consistent.
When refining, refinement gets stuck as I mentioned above.
I've run Phenix x-triage and the results include this line (see below): "It could be worthwhile considering reprocessing the data". I was wondering if the Multivariate Z score L-test: 6.305 might suggest how to reprocess the data.
Sorry for the probably trivial question and for probably missing important data.
Thanks a lot for any help and suggestions,
Claudia
------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data):
Statistics independent of twin laws - /^2 : 1.827 - ^2/ : 0.838 - : 0.649 - , : 0.417, 0.242 Multivariate Z score L-test: 6.305 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it.
No (pseudo)merohedral twin laws were found.
Patterson analyses - Largest peak height : 11.094 (correpsonding p value : 1.080e-01)
The largest off-origin peak in the Patterson function is 11.09% of the height of the origin peak. No significant pseudotranslation is detected.
The results of the L-test indicate that the intensity statistics are significantly different then is expected from good to reasonable, untwinned data. As there are no twin laws possible given the crystal symmetry, there could be a number of reasons for the departure of the intensity statistics from normality. Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems as well as bad data quality might be possible reasons. It could be worthwhile considering reprocessing the data. -----------------------------------------------------------------------------------------------
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673
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you probably need to refine a twin fraction as well.
phenix.refine might be of help.
P
2007/6/29, Claudia Scotti
Thank you so much.
I'll try all the space groups and see what happens.
Many thanks again,
Claudia
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673
----------------------------------------
Date: Fri, 29 Jun 2007 07:35:22 -0700 From: [email protected] To: [email protected] Subject: Re: [phenixbb] Multivariate Z score L-test
Hi Claudia,
This could indicate that tyour data is actually P 2 1 1, P 1 2 1 or P 1 1 2 or P 21 1 1, P 1 21 1, P 1 1 21. Try processing that data in those spacegroups and see if that makes any difference. You might end up havig to refine your structure in all spacegroups to find out which possibility is the best.
It could also indicate that the quality of your data is not very good, either due to suboptimal data processing or because of bad diffraction (or both).
HTH
Peter
2007/6/29, Claudia Scotti :
Dear List,
I'm only at my third structure (a scFv antibody fragment) and I'm disturbing about a dataset that is giving problems at the refinement stage: it gets stuck at about Rcryst= 0.36 and Rfree=0.44.
I've tried data processing with several softwares (Mosflm, XDS, Denzo) and the result is consistently P222, unit cell 69x79x90, 90, 90, 90. The data are anisotropic, with limits at 2.3 and 2.8 A. I cut the data at 3.0 A. Matthews coefficient suggests two molecules per asu. No NCS is detected by self-rotation and a native Patterson detects a small peak (10% of origin peak) at 0.19, 0.34, 0.5. MR using several softwares (AmoRe, Molrep and Phaser) and several models all agree that the best space group is P21212, though the systematic absences are not perfectly consistent.
When refining, refinement gets stuck as I mentioned above.
I've run Phenix x-triage and the results include this line (see below): "It could be worthwhile considering reprocessing the data". I was wondering if the Multivariate Z score L-test: 6.305 might suggest how to reprocess the data.
Sorry for the probably trivial question and for probably missing important data.
Thanks a lot for any help and suggestions,
Claudia
------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data):
Statistics independent of twin laws - /^2 : 1.827 - ^2/ : 0.838 - : 0.649 - , : 0.417, 0.242 Multivariate Z score L-test: 6.305 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data is expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not neccesarily exclude it.
No (pseudo)merohedral twin laws were found.
Patterson analyses - Largest peak height : 11.094 (correpsonding p value : 1.080e-01)
The largest off-origin peak in the Patterson function is 11.09% of the height of the origin peak. No significant pseudotranslation is detected.
The results of the L-test indicate that the intensity statistics are significantly different then is expected from good to reasonable, untwinned data. As there are no twin laws possible given the crystal symmetry, there could be a number of reasons for the departure of the intensity statistics from normality. Overmerging pseudo-symmetric or twinned data, intensity to amplitude conversion problems as well as bad data quality might be possible reasons. It could be worthwhile considering reprocessing the data. -----------------------------------------------------------------------------------------------
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673
_________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_________________________________________________________________ With Windows Live Hotmail, you can personalize your inbox with your favorite color. www.windowslive-hotmail.com/learnmore/personalize.html?locale=en-us&ocid=TXT_TAGLM_HMWL_reten_addcolor_0607 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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Claudia Scotti -
Peter Zwart