Re: [ccp4bb] Scalepack error model?
Hi Zbyszek, thanks for your reply! The scalepack log file gives the formula: Chi**2 = SUM ( (I - I) ** 2) / (Error ** 2 * N / (N-1) ) ) which equivalent to the Jay Ponder's formula, with the important addition, that sigma_avg and Iavg represent the average of all _other_ measurements with the same reduced hkl index. All sigmas are calculated from the error model described in the publications. So sigma_avg and I_avg in Ponder's formula are values that exclude the I_meas(hkl). That makes sense since we want the distributions of I_avg and I_meas to be independent. I'm still confused about how the Error value is calculated. What we want is the sigma that corresponds to the distribution of I_avg - I_meas values. As Ponder says this is sigma_avg^2 + sigma_meas^2. So I assume that sigma_avg is simply the calculated sigma of ALL the measured I's with the same reduced hkl index (no error model used for this term). The error model comes in with the sigma_meas term. That is calculated by scaling the measured sigma's from the integration with a factor derived from the error model. The error model as given in the International Tables F Eqs. (11.4.8.5-7) is W = 1/[(sig*E1)^2+( I_corr*E2)^2](5) I_corr = SUM (I_corr*W)/ SUM W (6) sig(I) = I/sqrt[SUM W] (7) So, to get sigma_meas above, presumably would use (7) for some I value (which one?). How does one compute the values of I_corr and W ? - Thanks Richard Gillilan MacCHESS Some of the error model parameters are defined at the moment by user, they can be refined iteratively by experimenter by adjusting parameters in subsequent runs of scalepack, but most of the time it is not required. New version will adjust all these parameters automatically. Zbyszek Otwinowski Richard Gillilan wrote: chi-2 = 1/N sum (I_avg - I_meas)^2/(sigma_avg^2 + sigma_meas^2)
Re: [ccp4bb] Density for pyrophosphate?
What you're seeing is not necessarily pyrophosphate. The negative difference density appears to concentrate around oxygen atoms most distant from the protein (and perhaps around the putative phosphorous atom?). Some clues might be obtained from e.g. the B-factor profile of the refined atoms. From the side-view pictures you sent it's not clear whether the density in question suports two tetrahedral ions... instead it could be two planar ions e.g. a malonate or some other molecule with two flat groups and a linker. Take a closer look at your omit difference density maps for starters. Does the positive difference density indicate the presence of a heavier atom in the center of a putative tetrahedron of lighter ones? Is one of the sides tetrahedral and the other - planar? Incidentally, if you compress the images you sent it's possible to get the size down from 3 MB each (encoded for email it's actually 4MB each!) down to about 60-100 KB each without significant loss of quality. I am sorry for bringing up my pet peeve but not everyone on this list enjoys 8 MB mass emails, especially when the contents do not justify the size in any way :) Artem -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Junyu Xiao Sent: Sunday, July 19, 2009 7:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Density for pyrophosphate? Dear all, I am at the late stage of refining a 1.97 A structure. There is something in the ligand binding pocket, and I am not sure what it is exactly. Since this protein can potentially generate pyrophosphate from ATP, and I have ATP in the protein solution, so I tried to fit in a pyrophosphate. The Rwork/Rfree after refinement are 0.198/0.243. Below is the refined map. The 2fofc map looks ok (contoured at 1 sigma), however, there is always some red density around the pyrophosphate in the fofc map (contoured at 3 sigma). I have also tried to fit in the density as two free phosphates, and the results are worse. Can I get some advices on this? Any suggestion will be greatly appreciated. Best regards, Junyu
Re: [ccp4bb] Density for pyrophosphate?
Could it be MPD (2-methyl-2,4-pentanediol)? Cheers, Charlie Junyu Xiao wrote: Dear all, I am at the late stage of refining a 1.97 A structure. There is something in the ligand binding pocket, and I am not sure what it is exactly. Since this protein can potentially generate pyrophosphate from ATP, and I have ATP in the protein solution, so I tried to fit in a pyrophosphate. The Rwork/Rfree after refinement are 0.198/0.243. Below is the refined map. The 2fofc map looks ok (contoured at 1 sigma), however, there is always some red density around the pyrophosphate in the fofc map (contoured at 3 sigma). I have also tried to fit in the density as two free phosphates, and the results are worse. Can I get some advices on this? Any suggestion will be greatly appreciated. Best regards, Junyu -- Charlie Bond Professorial Fellow University of Western Australia School of Biomedical, Biomolecular and Chemical Sciences M310 35 Stirling Highway Crawley WA 6009 Australia charles.b...@uwa.edu.au +61 8 6488 4406
