Thank you for your help,
I had the write rejection file set to 0.5 and probability at 0.001. It
seems that I had so many rejections that it was hard to get rid of all of
them. I have obtained a script to keep running scalepack until all of the
rejections are gone from the log file. It takes a very long time to run
but it is better than hitting enter over and over.
Although I have read the manual I am still having some difficulty
understanding the difference between rejection file and the probability.
If rejection file is set to 0.5 I'm guessing that if a reflection has a
50% probability of being an outlier it will be written to the log file.
But I don't understand how the rejection probability interplays here.
Thanks for any help you can provide.
-Yarrow
> Yarrow,
>
> as far as I know, scalepack, scalepackvirus and the other variants only
> differ by their respective array sizes (Someone from Wladek's or ZO's
> lab may be more suitable to comment on this). The rejections in the log
> file are controlled by the parameters 'write rejection file xxx' and
> 'rejection probability'. You may want to read up on those in the manual.
> I believe that historically the way it was supposed to work is that
> rejection candidates are written to the log file for examination and
> then in subsequent rounds are written to the 'reject' file. The latter
> is determined by the 'write rejection file' parameter.
>
> No, scalepack does not output the rmeas or rpim values. I have some
> recollection that Manfred Weiss at EMBL wrote a program which could
> analyze scalepack data written with 'no merge original index' to yield
> those parameters, you may want to look into this. The name of the
> fortran source is 'rmerge.f'. Unfortunately the link to the original
> source repository is dead, but I have a copy around, which I could
> share.
>
> Another way would be to go the route of scalepack unmerged data ->
> pointless -> scala, although I have never tried that myself.
>
> Good luck
>
> Carsten
>
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Yarrow Madrona
> Sent: Tuesday, December 06, 2011 11:04 AM
> To: [log in to unmask]
> Subject: [ccp4bb] scalepackvirus rejections and Rrin
>
> Hello,
>
> I am using scalepackvirus and I noticed that the rejection list grows
> but
> does not disappear in later rounds of scaling from the log file as in
> scalepack. I am assuming that the rejections are treated the same way as
> in scalepack but for some reason are not removed from the log file.
> Does
> anyone know if this is correct?
>
> Also I wondered if there is any way to get a redundancy dependent R
> value
> from scalepack. Thank you.
>
> -Yarrow
>
> --
> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
>
>
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
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