High R factor

From: Dipankar Manna
Date: 20 February 2012 10:48

Dear Sir/Madam,

 

I am very new to this CCP4 program. Usually I know that after rigid body refinement the R factor reduces from the R factor what ever we get from Molrep. One of my data is showing some different characteristics. After running Molrep the R factor is showing 38% and score is 64%, but when I run rigid body refinement (Refmac5) the Rfactor is showing 46.07% and Rfree is 46.27. is it possible? Or else what I have to do with this data.

 

Please suggest.

 

Regards

 

Dipankar Manna  

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From: Laurent Maveyraud

Hi,

it might well be possible that molrep used only lower resolution data (the default cutoff isd 2.5 A, if I remember correctly), when refmac uses all available data in the MTZ file...
Check that both steps were performed at the same resolution !

Another possibility is that molrep performed the search in different spacegroups than the one specified in the MTZ file (eg P4 selected during data processing, and molrep checks, P4, P41, P42 and P43). If your solution corresponds to the P41 spacegroup, you have to modify your MTZ file (or use the one produced by molrep)... otherwise refmac will perform the rigid body step in P4 and not P41...
This should be indicated in the molrep logfile... check it carefully !

hope this helps. If not please send the logfiles !

Laurent