Re: [ccp4bb] problem in scaling the Zn-MAD data
I don't see how a self rotation function can determine SG. If you processed data as P1 then found the SR maps showed 3 folds and 2 folds you might suspect that POINT GROUP!!! (Remember space groups are guessed on the basis of systematic absences - you don't really know that till you have a structure solution) At the integration stage it is important to choose a crystal class - e.g. trigonal with a=b and gamma = 120 The point groups then may be P3 P312 P321 P6 P6/mmm After integration a program like pointless checks for symmetry agreement. eg do h k l k (-h-k),l and -h-k,h,l agree well? In that case you probably have 3 fold symmetry. And so on for other possible symmetry operators.. After that you can probably be confident of your point group. But as Clemens pointed out - there are different equally possible indexing conventions for some of these choices. You need to check pass 2 against pass 1, etc - see pointless GUI Eleanor On Apr 5 2012, Deepthi wrote: Hello I arrived at the p312 space group by running a self rotation function using MOLREP. The maps show the space group as p312. I was scaling the data individually for each wavelength. None of the three wavelengths are scaling are scaling in p312 space group. On Thu, Apr 5, 2012 at 2:17 AM, Clemens Vonrhein wrote: Hi, On Wed, Apr 04, 2012 at 02:07:58PM -0700, Deepthi wrote: > Hello everyone I have a problem scaling the MAD data which was > collected a week ago.The data was collected at 1.5A resolution using > three wavelengths for Zn-MAD experiments. Scaling the data for MAD > experiments, the number of rejections > and chi2 values were very high even after adjusting the error-scale factor > and error model. The space group i used was p312 which i obtained by > running a self-rotation function in MOLREP. When i scale my data using p312 > spacegroup the chi2 and rejections were huge. But he data was scaling well > in p321 spacegroup. can anyone explain whats going on? When you say 'Scaling the data for MAD experiments': do you mean scaling the various scans for your 3-wvl MAD data in a single scaling job? Unless you already took care of this during data integration, remember that your separate scans could have been indexed differently and therefore don't match up. See eg. http://www.ccp4.ac.uk/html/reindexing.html for some lookup-tables in P312 and P321. You can use the CCP4 program 'reindex' on MTZ files if needed. But I guess most modern data-processing and scaling programs will take care of that automatically anyway? Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) *** -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] problem in scaling the Zn-MAD data
You know that point group has two indexing conventions (h k l and -k,-h,-l if I remember - see the CCP4 documentation on alternate indexing and use pointless to sort it out.. Eleanor . Use pointless to check On Apr 4 2012, Deepthi wrote: Hello everyone I have a problem scaling the MAD data which was collected a week ago.The data was collected at 1.5A resolution using three wavelengths for Zn-MAD experiments. Scaling the data for MAD experiments, the number of rejections and chi2 values were very high even after adjusting the error-scale factor and error model. The space group i used was p312 which i obtained by running a self-rotation function in MOLREP. When i scale my data using p312 spacegroup the chi2 and rejections were huge. But he data was scaling well in p321 spacegroup. can anyone explain whats going on? Thank you very much Deepthi -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266
Re: [ccp4bb] problem in scaling the Zn-MAD data
Hi - Let me just add that P312 is a very uncommon space group for protein crystals, much less common than P321. (This doesn't mean you don't have it - it's just unlikely.) If you look at PDB statistics: P 3 1 2 : 12 structures P3(1) 1 2: 61 structures P3(2) 1 2: 85 structures P 3 2 1 : 278 structures P3(1) 2 1: 2354 structures P3(2) 2 1: 2533 structures This also suggests, by the way, that you have a screw axis that you haven't accounted for yet. It won't affect your data scaling, but it sure will affect your molecular replacement job! Hope that helps, Matt On 4/5/12 12:31 PM, Deepthi wrote: Hello I arrived at the p312 space group by running a self rotation function using MOLREP. The maps show the space group as p312. I was scaling the data individually for each wavelength. None of the three wavelengths are scaling are scaling in p312 space group. On Thu, Apr 5, 2012 at 2:17 AM, Clemens Vonrhein mailto:vonrh...@globalphasing.com>> wrote: Hi, On Wed, Apr 04, 2012 at 02:07:58PM -0700, Deepthi wrote: > Hello everyone > I have a problem scaling the MAD data which was collected a week ago.The > data was collected at 1.5A resolution using three wavelengths for Zn-MAD > experiments. Scaling the data for MAD experiments, the number of rejections > and chi2 values were very high even after adjusting the error-scale factor > and error model. The space group i used was p312 which i obtained by > running a self-rotation function in MOLREP. When i scale my data using p312 > spacegroup the chi2 and rejections were huge. But he data was scaling well > in p321 spacegroup. can anyone explain whats going on? When you say 'Scaling the data for MAD experiments': do you mean scaling the various scans for your 3-wvl MAD data in a single scaling job? Unless you already took care of this during data integration, remember that your separate scans could have been indexed differently and therefore don't match up. See eg. http://www.ccp4.ac.uk/html/reindexing.html for some lookup-tables in P312 and P321. You can use the CCP4 program 'reindex' on MTZ files if needed. But I guess most modern data-processing and scaling programs will take care of that automatically anyway? Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) *** -- Deepthi -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165
Re: [ccp4bb] problem in scaling the Zn-MAD data
Hello I arrived at the p312 space group by running a self rotation function using MOLREP. The maps show the space group as p312. I was scaling the data individually for each wavelength. None of the three wavelengths are scaling are scaling in p312 space group. On Thu, Apr 5, 2012 at 2:17 AM, Clemens Vonrhein wrote: > Hi, > > On Wed, Apr 04, 2012 at 02:07:58PM -0700, Deepthi wrote: > > Hello everyone > > I have a problem scaling the MAD data which was collected a week ago.The > > data was collected at 1.5A resolution using three wavelengths for Zn-MAD > > experiments. Scaling the data for MAD experiments, the number of > rejections > > and chi2 values were very high even after adjusting the error-scale > factor > > and error model. The space group i used was p312 which i obtained by > > running a self-rotation function in MOLREP. When i scale my data using > p312 > > spacegroup the chi2 and rejections were huge. But he data was scaling > well > > in p321 spacegroup. can anyone explain whats going on? > > When you say 'Scaling the data for MAD experiments': do you mean > scaling the various scans for your 3-wvl MAD data in a single scaling > job? Unless you already took care of this during data integration, > remember that your separate scans could have been indexed differently > and therefore don't match up. See eg. > > http://www.ccp4.ac.uk/html/reindexing.html > > for some lookup-tables in P312 and P321. You can use the CCP4 program > 'reindex' on MTZ files if needed. > > But I guess most modern data-processing and scaling programs will take > care of that automatically anyway? > > Cheers > > Clemens > > -- > > *** > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com > * > * Global Phasing Ltd. > * Sheraton House, Castle Park > * Cambridge CB3 0AX, UK > *-- > * BUSTER Development Group (http://www.globalphasing.com) > *** > -- Deepthi
Re: [ccp4bb] problem in scaling the Zn-MAD data
Hi, On Wed, Apr 04, 2012 at 02:07:58PM -0700, Deepthi wrote: > Hello everyone > I have a problem scaling the MAD data which was collected a week ago.The > data was collected at 1.5A resolution using three wavelengths for Zn-MAD > experiments. Scaling the data for MAD experiments, the number of rejections > and chi2 values were very high even after adjusting the error-scale factor > and error model. The space group i used was p312 which i obtained by > running a self-rotation function in MOLREP. When i scale my data using p312 > spacegroup the chi2 and rejections were huge. But he data was scaling well > in p321 spacegroup. can anyone explain whats going on? When you say 'Scaling the data for MAD experiments': do you mean scaling the various scans for your 3-wvl MAD data in a single scaling job? Unless you already took care of this during data integration, remember that your separate scans could have been indexed differently and therefore don't match up. See eg. http://www.ccp4.ac.uk/html/reindexing.html for some lookup-tables in P312 and P321. You can use the CCP4 program 'reindex' on MTZ files if needed. But I guess most modern data-processing and scaling programs will take care of that automatically anyway? Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] problem in scaling the Zn-MAD data
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Deepthi, is it just a typo, or do your last two sentences say that your data DO NOT scale in P312 but scale well in P321? Did you try pointless for space group determination? I have not used molrep for this purpose and cannot judge how reliable the self rotation function is for space group determination. Depending on your resolution and cell dimensions you may have very few reflection for determining the screw axis. Do your data suffer from radiation damage, does the cell become greater during integration? Did you fix the detector distance during integration? Best wishes, Tim On 04/04/12 23:07, Deepthi wrote: > Hello everyone > I have a problem scaling the MAD data which was collected a week ago.The > data was collected at 1.5A resolution using three wavelengths for Zn-MAD > experiments. Scaling the data for MAD experiments, the number of rejections > and chi2 values were very high even after adjusting the error-scale factor > and error model. The space group i used was p312 which i obtained by > running a self-rotation function in MOLREP. When i scale my data using p312 > spacegroup the chi2 and rejections were huge. But he data was scaling well > in p321 spacegroup. can anyone explain whats going on? > > Thank you very much > > Deepthi > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPfVx7UxlJ7aRr7hoRAlLbAJ0XPZq/SmucWYEuzYSHAZBzYTbJIwCeI1oY IyoLBnvHizxqj5oDGA/JY3s= =cKSs -END PGP SIGNATURE-
Re: [ccp4bb] problem in scaling the Zn-MAD data
Sounds then like your spacegroup is p321... It's your data (scaling) that determines that, not your preconceptions (which wasn't clear how arrived at either?) cheers Phx Sent from tiny silly touch screen - Reply message - From: "Deepthi" Date: Wed, Apr 4, 2012 22:07 Subject: [ccp4bb] problem in scaling the Zn-MAD data To: Hello everyone I have a problem scaling the MAD data which was collected a week ago.The data was collected at 1.5A resolution using three wavelengths for Zn-MAD experiments. Scaling the data for MAD experiments, the number of rejections and chi2 values were very high even after adjusting the error-scale factor and error model. The space group i used was p312 which i obtained by running a self-rotation function in MOLREP. When i scale my data using p312 spacegroup the chi2 and rejections were huge. But he data was scaling well in p321 spacegroup. can anyone explain whats going on? Thank you very much Deepthi
[ccp4bb] problem in scaling the Zn-MAD data
Hello everyone I have a problem scaling the MAD data which was collected a week ago.The data was collected at 1.5A resolution using three wavelengths for Zn-MAD experiments. Scaling the data for MAD experiments, the number of rejections and chi2 values were very high even after adjusting the error-scale factor and error model. The space group i used was p312 which i obtained by running a self-rotation function in MOLREP. When i scale my data using p312 spacegroup the chi2 and rejections were huge. But he data was scaling well in p321 spacegroup. can anyone explain whats going on? Thank you very much Deepthi
