That result looks really bizarre but it is hard to make a sensible comment
without more details..maybe you could attach the whole log file for the
refmac run.
What input reflection dAta are you using ? You couldn’t have picked up a
Sharpened set by any chance? (It is always good practice to make sure you
are using the original merged set.)
Good luck Eleanor
On Sat, 27 Apr 2024 at 07:39, Kay Diederichs <kay.diederi...@uni-konstanz.de>
wrote:
> 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 <martin.mo...@ki.se>
> 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.
> >
> >Head of Macromolecular X-ray Crystallography<https://ki.se/en/mbb/psf-mx>
> | Protein Science Facility<https://ki.se/en/mbb/protein-science-facility>
> >Medical Biochemistry and Biophysics<
> https://ki.se/en/mbb/department-of-medical-biochemistry-and-biophysics>
> >171 65 Solna | Solnav
> <https://www.google.com/maps/search/171+65+Solna+%7C+Solnav?entry=gmail&source=g>�gen
> 9
> >+46 8 524 868 43 | +46 73 322 93 27
> >martin.mo...@ki.se<mailto:martin.mo...@ki.se> | ki.se<https://ki.se/>
> >______________________________________
> >[cid:image001.png@01DA9812.F040E8F0]<https://ki.se/psf
> >[cid:image002.jpg@01DA9812.F040E8F0]<https://gu.se/pps>
> [cid:image003.png@01DA9812.F040E8F0] <https://ki.se/>
> >
> >
> >
> >
> >
> >N�r du skickar e-post till Karolinska Institutet (KI) inneb�r detta att
> KI kommer att behandla dina personuppgifter. H�r finns information om hur
> KI behandlar personuppgifter<https://ki.se/om-ki/integritetsskyddspolicy>.
> >
> >
> >Sending email to Karolinska Institutet (KI) will result in KI processing
> your personal data. You can read more about KI's processing of personal
> data here<https://staff.ki.se/data-protection-policy>.
> >
> >########################################################################
> >
> >To unsubscribe from the CCP4BB list, click the following link:
> >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >
>
> ########################################################################
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
