Dear Martin,
one suspicion comes to my mind: could it be a "computer problem" in the sense that you are using different computing environments for the two calculations (arpWarp vs standalone refmac5)? That could lead to different decimal separators ("." versus a ","; see https://en.wikipedia.org/wiki/Decimal_separator ). This could happen for
- different computers or operating systems
- different users, because each user can set the LANG individually
In my experience with this problem, it shows e.g. in coot by distorted bonds and the like. And I do see in your screenshot that the coordinates differ between your two runs.
The workaround is to set the LANG to C:
export LANG=C
if you use the bash shell (similarly in other shells), before starting calculations.
Anyway, you could report which computing environment you use, maybe that gives a hint.
Hope this helps,
Kay
On Fri, 26 Apr 2024 17:59:07 +0000, Martin Moche <[log in to unmask]> wrote:
>Dear CCP4bb,
>
>I have a high resolution 1.4� dataset, and running arpWarp after MR and make almost all model building required.
>
>After arpWarp, my model and data fit excellent to each other, R-value around 20, and a few residues in the terminii remains to be fixed.
>
>When I send the output from arpWarp to refmac5, the B-factor column gets corrupted pictures in attached PDF, and R/Rfree increase to 0.26/0.28 and "Correlation Coefficient Fo-Fc" are also worsening.
>
>The arpWarp routine uses the same refmac5 version 5.8.0425 as "refmac5 itself".
>
>I tried refmac5 in both CCP4 017 and 019, using the same refmac5 version 5.8.0425, and B-factor column gets corrupted in both.
>
>Best regards,
>Martin
>
>P.S.
>phenix.refine has no problems and R/Rfree remains at 0.20/0.22...
>D.S.
>
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