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EEK, it seems to me that anything called simply "FP" should be unadulterated FP. If the software modifies a column in some way, it should give it a new label, shouldn't it?
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Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago773 834 1723; [log in to unmask]
http://bmb.bsd.uchicago.edu/Faculty_and_Research/
From: CCP4 bulletin board [[log in to unmask]] on behalf of Eleanor Dodson [[log in to unmask]]
Sent: Wednesday, July 17, 2013 6:05 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] TLS refinement refmac
EleanorOr are you doing several cycles of refinement in thesecond pass too - in that case one would hope the Rfactor would continue to fall.Oh dear - you should always start refinement against the original processed data - but others have told you that already..The TLS files will not be appropriate for the rescaled FPs - it is surprising that the Rfactor actually goes down though!
On 17 July 2013 11:00, Guenter Fritz <[log in to unmask]> wrote:
Am 17.07.2013 11:59, schrieb Guenter Fritz:
Hi Stefan and Gottfried,
thanks a lot for the answers. This is the point. Wouldn't it make more sense to add an extra column that contains the changed Fs?
Best, Guenter
Hi,
it is strongly advised to use the original mtz e.g. scala.mtz as the refmac input mtz in all refmac runs,
as this contains the original Fs - Refmac applies some aniso corrections to the Fs and puts them into the output.mtz.
so the output Fs are not the same as in the input F - therefore one should use the scala.mtz
cheers
Stefan
-----Ursprüngliche Nachricht-----
Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Guenter Fritz
Gesendet: Mittwoch, 17. Juli 2013 10:39
An: [log in to unmask]
Betreff: [ccp4bb] TLS refinement refmac
Dear all,
one gets different R values, if you re-read in the mtz written out by refmac after TLS refinement. I think this issue had been a while ago in ccp4bb, but I can't find the right track.
Here are the details.
1st run:
If we do TLS + restr. refinement in refmac we get:
Initial Final
R factor 0.3010 0.2170
R free 0.3175 0.2695
2nd run:
Now, if we use the same input pdb and the same input tls paramter file, but use the mtz written out by the first run, we get:
Initial Final
R factor 0.2274 0.1903
R free 0.2482 0.2540
Apparently in the mtz file written out by the 1st refmac must contain
some information that is re-read in the 2nd run. But one just defines
FP, SIGFP and Rfree flags. Do FPs change in the output mtz after TLS
refinement??
Any help to clarify this is appreciated.
Thanks, Guenter