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�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/
