Re: [ccp4bb] Determining Rpim value
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Michelle, unless any of the HKL2000 log files list Rpim, ALL your options involve going back to obtaining umerged intensities. If you still have the x-files available, the easiest from my point of view is to use x2sad followed by sadabs and xprep. xprep has a menu entry to show Rpim. Having said that, the (non-)availability of sadabs is probably the bottle neck in this chain, I am afraid. Cheers, Tim On 09/05/2012 12:14 AM, Michelle Deaton wrote: I am trying to obtain an Rpim (precision indicating merging Rfactor) value for a dataset that I have already processed with HKL2000/Scalepack and refined. Is there a straightforward way to obtain this value from my data? From what I understand, most of my options involve going back and obtaining unmerged intensities. I am hoping there may be a way for me to avoid having to backtrack that far, as this data is now very far along in the refinement process. Thank you, Michelle Deaton University of Denver Department of Chemistry and Biochemistry - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQRwpnUxlJ7aRr7hoRAsdIAJ4qkETGL+eIdyu3v/jLdE5qTlA17wCg60Sn ezz/NHQXNakdUUKuBbqrs6g= =9gjj -END PGP SIGNATURE-
Re: [ccp4bb] Determining Rpim value
Michelle, On 09/04/2012 06:14 PM, Michelle Deaton wrote: Is there a straightforward way to obtain this value from my data? From what I understand, most of my options involve going back and obtaining unmerged intensities. I am hoping there may be a way for me to avoid having to backtrack that far, as this data is now very far along in the refinement process. The simple answer is no, you cannot avoid going back to unmerged data, because the variation among redundant measurements is what Rpim etc reflects, and once that information is gone upon merging, it's gone. As others have pointed out, you can either a) run scalepack with NO MERGE ORIGINAL INDEX option and then use scala. There was also a separate program called RMERGE by Manfred Weiss, but the embl link does not work. For this, you need at least the original denzo output, i.e. *.x files. b) if you have original images, you can use mosflm/scala or xds/scala to re-process your data. (Then choose the one that gave you the lowest R-value ;) Perhaps one day scalepack will report Rpim. Cheers, Ed.
[ccp4bb] Determining Rpim value
I am trying to obtain an Rpim (precision indicating merging Rfactor) value for a dataset that I have already processed with HKL2000/Scalepack and refined. Is there a straightforward way to obtain this value from my data? From what I understand, most of my options involve going back and obtaining unmerged intensities. I am hoping there may be a way for me to avoid having to backtrack that far, as this data is now very far along in the refinement process. Thank you, Michelle Deaton University of Denver Department of Chemistry and Biochemistry
Re: [ccp4bb] Determining Rpim value
If the alternative to reprocessing your data with XDS, iMosflm, Xia2, autoProc etc is unpalatable, might I suggest the nearly-as-unpalatable method as follows: If you can still run Scalepack on all your .x files, put the line NO MERGE ORIGINAL INDEX in the scalepack script file. Get the .sca or .hkl file out of that. Use the following - strictly no warranties - script: # Assumes scalepack.hkl is created with NO MERGE ORIGINAL INDEX # # pointless SCAIN scalepack.hkl HKLOUT scalepack.mtz EOF NAME PROJECT mydata CRYSTAL mydata1 CELL 75.2 75.2 135.890.00090.00090.000 EOF # # scala hklin scalepack.mtz hklout scala.mtz \ scales scala.scales \ rogues scala.rogues \ normplot scala.norm \ anomplot scala.anom EOF bins 20 resolution 2.9 run 1 all resolution run 1 high 2.9 name run 1 project AUTOMATIC crystal DEFAULT dataset scalepack scales constant exclude sdmin 2.0 sdcorrection fixsdb noadjust norefine both 1.0 0.0 anomalous off EOF Corrections, comments or outright repudiation of this script quite welcome - this was my first attempt. Phil Jeffrey Princeton On 9/4/12 6:14 PM, Michelle Deaton wrote: I am trying to obtain an Rpim (precision indicating merging Rfactor) value for a dataset that I have already processed with HKL2000/Scalepack and refined. Is there a straightforward way to obtain this value from my data? From what I understand, most of my options involve going back and obtaining unmerged intensities. I am hoping there may be a way for me to avoid having to backtrack that far, as this data is now very far along in the refinement process. Thank you, Michelle Deaton University of Denver Department of Chemistry and Biochemistry
