Re: [ccp4bb] MAD data process problem
Thank you very much for your reply. In my own understanding, We collect the peak dataset, because of the large F'', and we can get strong anomalous signal. We collect the edge dataset, because of the large F', and combined with the remote dataset, we can use the method just like SIR to get some information about the phase. so I think for peak dataset, anomalous processing is necessary, and for edge and remote dataset, anomalous processing is not necessary. Is my understanding correct? Thank you very much for your help. Best wish, Qixu Cai 2012/5/29 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qixu Cai, MAD phasing is based on the comparison of Bijvoet-pairs, i.e. I(hkl) with I(-h-k-l), both within one data set and between data sets. Therefore you might get better results if your integration program does not assume Friedel-pairs to have identical intensities, even though the difference is probably only marginal (integration programs do not merge data). So it is safest click on 'anomalous' for all data sets involved . Tim On 05/29/12 11:11, Qixu Cai wrote: Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai - -- - -- 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/ iD8DBQFPxJfaUxlJ7aRr7hoRAm3EAKCKkyvT8z0wg6MFjflkHkiq8RR5GQCgyvF3 lOIOLypSzCcN3N6OR/3NcC8= =m6ax -END PGP SIGNATURE-
Re: [ccp4bb] MAD data process problem
Hi, you are right, the peak dataset corresponds to the highest f'' value. However, this does not mean that f'' is null for the other wavelengthes... you still have significant anomalous signal at the edge and for the high energy remote wavelength... this will help your phasing, so use it ! As Tim mentionned it : process all wavelength with anomalous switched on ! laurent Le 30/05/2012 07:59, Qixu Cai a écrit : Thank you very much for your reply. In my own understanding, We collect the peak dataset, because of the large F'', and we can get strong anomalous signal. We collect the edge dataset, because of the large F', and combined with the remote dataset, we can use the method just like SIR to get some information about the phase. so I think for peak dataset, anomalous processing is necessary, and for edge and remote dataset, anomalous processing is not necessary. Is my understanding correct? Thank you very much for your help. Best wish, Qixu Cai 2012/5/29 Tim Gruene t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qixu Cai, MAD phasing is based on the comparison of Bijvoet-pairs, i.e. I(hkl) with I(-h-k-l), both within one data set and between data sets. Therefore you might get better results if your integration program does not assume Friedel-pairs to have identical intensities, even though the difference is probably only marginal (integration programs do not merge data). So it is safest click on 'anomalous' for all data sets involved . Tim On 05/29/12 11:11, Qixu Cai wrote: Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai - -- - -- 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/ iD8DBQFPxJfaUxlJ7aRr7hoRAm3EAKCKkyvT8z0wg6MFjflkHkiq8RR5GQCgyvF3 lOIOLypSzCcN3N6OR/3NcC8= =m6ax -END PGP SIGNATURE- -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] MAD data process problem
Dear Qixu Cai, The following paper should be informative for your query:- http://dx.doi.org/10.1107/S0909049595013288 Best wishes, John Prof John R Helliwell DSc On 29 May 2012, at 10:11, Qixu Cai caiq...@gmail.com wrote: Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai
[ccp4bb] MAD data process problem
Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai
Re: [ccp4bb] MAD data process problem
Hi, when processing MAD data, all wavelength should be processed without enforcing the Friedel's law... If you look at your fluorescence spectrum, you will see that you have anomalous signal for the peak (obviously) for the high energy remote and even forh the inflexion point. For example, in the case of Se-MAD : peak : f'=-6, f''-8 inflexion : f'=-11, f''= 4 high remote : f'= -4, f''= 4 the low energy remote is the one with the weakest anamalous signal, close to 0 in the case of Se... hope this helps laurent Le 29/05/2012 11:11, Qixu Cai a écrit : Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] MAD data process problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qixu Cai, MAD phasing is based on the comparison of Bijvoet-pairs, i.e. I(hkl) with I(-h-k-l), both within one data set and between data sets. Therefore you might get better results if your integration program does not assume Friedel-pairs to have identical intensities, even though the difference is probably only marginal (integration programs do not merge data). So it is safest click on 'anomalous' for all data sets involved . Tim On 05/29/12 11:11, Qixu Cai wrote: Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai - -- - -- 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/ iD8DBQFPxJfaUxlJ7aRr7hoRAm3EAKCKkyvT8z0wg6MFjflkHkiq8RR5GQCgyvF3 lOIOLypSzCcN3N6OR/3NcC8= =m6ax -END PGP SIGNATURE-
