[ccp4bb] pseudo-translation vector in molrep
Dear colleagues, For a particular MR problem I am dealing with, 'analyse_mr' suggests that there maybe a pseudo-translation vector as evidenced by the very significant non-origin peaks in the native patterson: e.g GRID 80 112 80 CELL 104.8290 151.2840 109.4910 90. 118.1310 90. ATOM1 Ano 0. 0. 0. 181.08 0.0 BFAC 20.0 ATOM2 Ano 0.9483 0. 0.0106 46.89 0.0 BFAC 20.0 ATOM3 Ano 0.0517 0. 0.9875 46.89 0.0 BFAC 20.0 ATOM4 Ano 0.9494 0.9911 0.0090 40.66 0.0 BFAC 20.0 ATOM5 Ano 0.0506 0.9911 0.9875 40.66 0.0 BFAC 20.0 ATOM6 Ano 0.0572 0.9911 0. 37.26 0.0 BFAC 20.0 BALBES also reports a pseudo-translation vector at 0.951 0.000 0.007, i.e. very similar to the output from 'analyse_mr'. Yet, Molrep fails to recognize this possibility (in auto' mode for the PST) claiming that the 0.125 limit for the peak height compared to the origin has not been reached. When I look at the output from 'analyse_mr' it is quite clear the peak is at 0.25 of the origin peak. Why is there such a discrepancy in the interpretation of the native patterson map? Best regards Savvas Savvas N. Savvides [EMAIL PROTECTED] for Structural Biology and Biophysics Laboratory for Protein Biochemistry - Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 Email: [EMAIL PROTECTED] http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html
Re: [ccp4bb] pseudo-translation vector in molrep
I think the error is in BALBES - there is a peak I guess at 0.95 0 0.01 but it must be too close to the origin to be a translation vector from one molecule to another. There are reasons for such peaks - sometimes spurious large terms in the data.. but they dont usually represent true molecular translations. Trust MOLREP! Eleanor Savvas Savvides wrote: Dear colleagues, For a particular MR problem I am dealing with, 'analyse_mr' suggests that there maybe a pseudo-translation vector as evidenced by the very significant non-origin peaks in the native patterson: e.g GRID 80 112 80 CELL 104.8290 151.2840 109.4910 90. 118.1310 90. ATOM1 Ano 0. 0. 0. 181.08 0.0 BFAC 20.0 ATOM2 Ano 0.9483 0. 0.0106 46.89 0.0 BFAC 20.0 ATOM3 Ano 0.0517 0. 0.9875 46.89 0.0 BFAC 20.0 ATOM4 Ano 0.9494 0.9911 0.0090 40.66 0.0 BFAC 20.0 ATOM5 Ano 0.0506 0.9911 0.9875 40.66 0.0 BFAC 20.0 ATOM6 Ano 0.0572 0.9911 0. 37.26 0.0 BFAC 20.0 BALBES also reports a pseudo-translation vector at 0.951 0.000 0.007, i.e. very similar to the output from 'analyse_mr'. Yet, Molrep fails to recognize this possibility (in auto' mode for the PST) claiming that the 0.125 limit for the peak height compared to the origin has not been reached. When I look at the output from 'analyse_mr' it is quite clear the peak is at 0.25 of the origin peak. Why is there such a discrepancy in the interpretation of the native patterson map? Best regards Savvas Savvas N. Savvides [EMAIL PROTECTED] for Structural Biology and Biophysics Laboratory for Protein Biochemistry - Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 Email: [EMAIL PROTECTED] _http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html_
Re: [ccp4bb] pseudo-translation vector in molrep
Hi, I suggest you check which version of MOLREP you used. Currently, BALBES now actually use MOLREP in 'auto' mode for PST. The two should be the same. The difference may be because BALBES uses the latest version of MOLREP. Fei On 7/30/07, Eleanor Dodson [EMAIL PROTECTED] wrote: I think the error is in BALBES - there is a peak I guess at 0.95 0 0.01 but it must be too close to the origin to be a translation vector from one molecule to another. There are reasons for such peaks - sometimes spurious large terms in the data.. but they dont usually represent true molecular translations. Trust MOLREP! Eleanor Savvas Savvides wrote: Dear colleagues, For a particular MR problem I am dealing with, 'analyse_mr' suggests that there maybe a pseudo-translation vector as evidenced by the very significant non-origin peaks in the native patterson: e.g GRID 80 112 80 CELL 104.8290 151.2840 109.4910 90. 118.1310 90. ATOM1 Ano 0. 0. 0. 181.08 0.0 BFAC 20.0 ATOM2 Ano 0.9483 0. 0.0106 46.89 0.0 BFAC 20.0 ATOM3 Ano 0.0517 0. 0.9875 46.89 0.0 BFAC 20.0 ATOM4 Ano 0.9494 0.9911 0.0090 40.66 0.0 BFAC 20.0 ATOM5 Ano 0.0506 0.9911 0.9875 40.66 0.0 BFAC 20.0 ATOM6 Ano 0.0572 0.9911 0. 37.26 0.0 BFAC 20.0 BALBES also reports a pseudo-translation vector at 0.951 0.000 0.007, i.e. very similar to the output from 'analyse_mr'. Yet, Molrep fails to recognize this possibility (in auto' mode for the PST) claiming that the 0.125 limit for the peak height compared to the origin has not been reached. When I look at the output from 'analyse_mr' it is quite clear the peak is at 0.25 of the origin peak. Why is there such a discrepancy in the interpretation of the native patterson map? Best regards Savvas Savvas N. Savvides [EMAIL PROTECTED] for Structural Biology and Biophysics Laboratory for Protein Biochemistry - Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 Email: [EMAIL PROTECTED] _http://www.eiwitbiochemie.ugent.be/units_en/structbio_en.html_
