Hi, Peter, Does the radition damage have such a large effect? There are many positive peaks seeing from the difference map, seems abnormal. But I have seen such difference maps before which are OK for modeling and refining.
Actually when I try to modelling the Se-met into the positive peaks, the R and free_R factor goes up about 2%. Does the occupancy of the Se affect the R factor, or should I change the occupancy? Another problem is f' andf f" prime, which I refine them when phasing with Solve. Actually, I did not use the same free set when refining with the native data and peak data.I try to compare them because I want to make it clear that the difference may be caused by the mad data while not the model itself. Thanks. > Hi Peng Zhang, > > The presence of radiation damage might cause some problems. > Do so see any obvious features in the difference map? > > Another problem (although I doubt it would cause such a big difference) > might be the fact that f' andf f" prime are incorrect. > Try and refine them (CNS or phenix.refine) maybe. > > Does your native data have the same free set as the peak data? if not, you > are in trouble and have to start from scratch with your native data to be > able to make a fair comparison. The 22/25 for 2.7 A seems awfully close > together. > > procheck has not very up to date standards of what is good and what is > not. Better use molprobity, available from: > > http://molprobity.biochem.duke.edu/ > > HTH > > Peter > > > > > > > > > > ----- Original Message ----- > From: Peng Zhang <[EMAIL PROTECTED]> > Date: Tuesday, March 20, 2007 6:04 pm > Subject: Re: [ccp4bb] modelling with sad/mad data > To: CCP4BB@JISCMAIL.AC.UK > >> Maybe I did not make the questions clear, which leading to the >> misleadings.Firstly, I have collected the mad data and get the >> phase at synchrotron, >> the phased Se is quite good for modelling, and get over 70% of the >> molecule run with resolve autobuilding.The density seems also good for >> building. But when finally refining the model, the gap between the >> R(0.22)and free_R(0.32 )is big, even though modelled the Se- >> methionine. Before >> collecting the mad data at synchrotron, I already have another >> native data >> set collected at home diffractometer (rigku, with R-axis IV++). To my >> surprise, when I using the same model(first model) and run with >> this data >> set, it is quite good( with 2.7A resolution, R=0.24 and Rf=0.28 and >> further refine to R=0.22 and Free_R=0.25), and I got the final >> model.Thegeometry of the first model and final model(actually no >> big difference of >> the two models)is quite good with procheck.The omit map says good >> enoughwith both of the two models. >> >> So I wondering what happened with the peak data? Did the anomolous >> signalhave much effect on the data? and anyone have the similar >> experience? >> >> > First it is always best to refine your model against the highest >> > resolution good quality data that you have available. There was >> > correspondence about the geometric weighting - could you have >> weighted> the Xray data too high and have bad geometry - see >> previous Emails! >> > >> > And the Free R seems rather low for the Se data. >> > Did you transfer the same Free R set from the native to the Se data? >> > Eleanor >> > >> > >> > Peng Zhang wrote: >> >> Dear friends, >> >> >> >> Recently, I have solved a structure using mad method. When >> using the >> >> peak >> >> data(2.3A) as the native for structure refinement, the gap >> between R >> >> factor and R free is big, about 0.1(0.22 and 0.32). I modelled the >> >> selenomethionine but the gap still exists. When I changed the >> data for a >> >> real native one(2.7A),it seems OK with R=0.24 and Rf=0.28. >> >> >> >> Does anyone have the similar experience? >> >> what should I pay attention to when using the sad/mad data as >> the native >> >> one for modelling and refinement? >> >> >> >> Thanks in advance. >> >> >> >> >> >> >> > >> > >> > >> >> >> -- >> Peng Zhang, Ph.D. Student >> Institute of Biochemistry and Cell Biology >> Shanghai Institutes for Biological Sciences >> Chinese Academy of Sciences >> >> 320 Yue-Yang Road >> Shanghai 20031 >> P.R. China >> >> >> >> Tel: 021-5492-1117 >> Fax: 021-5492-1116 >> Email: [EMAIL PROTECTED] >> > > -- Peng Zhang, Ph.D. Student Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 20031 P.R. China Tel: 021-5492-1117 Fax: 021-5492-1116 Email: [EMAIL PROTECTED]
