Dear colleagues, I would like to thank J. Murray, J. Wright, K. Futterer, E. Dodson, A. Forster, and F. Long for responding to my posting of two days ago on pseudo-translation vectors in molrep vs other programs (see original posting at the end of this message). I should have said at the outset that we are dealing with a limiting data set (see stats below), but since this is the only data we were ever able to collect on this membrane protein, we have no option but to milk it as much as we can.
P21 with 104.82 151.28 109.49 90.00 118.13 90.00 Resolution: 30-4.2 angs (4.3-4.2) Rmeas=0.15 (0.380) I/sigma: 7.2 (1.9) Completeness=93% (75%) Redundancy= 2.3 (2.1) Mosaicity= 1.1 deg High data anisotropy, primarily along the K reciprocal axis. The comments from Eleanor Dodson and Klaus Futterer prompted me to take another look at the data frame per frame. I concluded that in several frames there were a few reflections in the 40-30 angs range that obviously did not fit my spot-integration strategy very well. After failing repeatedly to get them to integrate acceptably without compromising the rest of the data too much, I decided to exclude all reflections between 40 and 30 angs res. This has resulted in three important improvements: (1) Better data integration and scaling statistics across the board. (1) The spurious peaks clustering around the origin in the native patterson are fewer, and those that do remain have a peak-height around 10-12% of the origin. (2) The new data set has yielded unambiguous peaks in the self-rotation function consistent with a 2-fold NCS axis. I have now used this SRF peak in MolRep and came up with a reasonable MR solution. I will soon try to implement this SRF info in PHASER as well via the "Rotate around" option. Best regards Savvas ---- Savvas N. Savvides Unit 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 > > 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 90.0000 118.1310 90.0000 > > ATOM1 Ano 0.0000 0.0000 0.0000 181.08 0.0 BFAC 20.0 > > ATOM2 Ano 0.9483 0.0000 0.0106 46.89 0.0 BFAC 20.0 > > ATOM3 Ano 0.0517 0.0000 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 0.0000 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
