Dear Ethan,
thanks for your fast answer. The pdb file does the trick. I also did not click
the reset B-factor box, which I thought is equivalent to the TLS+Biso pdb. Is
that wrong?
Every program has his special requirements and I mixed it up with a refinement
done some weeks before in phenix.
I'm sorry about that and thanks again for your help
Christian
Am Montag 11 Oktober 2010 19:50:10 schrieb Ethan Merritt:
> On Monday, October 11, 2010 11:01:10 am Christian Roth wrote:
> > Dear all,
> >
> > I want refine my model using TLS plus phase information from experimental
> > phases.
> > I used the TLSMD server to generate the initial tls parameters and
> > started Refmac
>
> I don't know exactly what has gone wrong.
> Let's collect some more information.
>
> - When you took the intial TLS parameters from TLSMD server, did you also
> take the corresponding modified PDB file?
> If not, that could well be the problem.
>
> - It looks from the output that you did not tick the "reset B factors to
> 20" box in ccp4i. Can you confirm that?
>
> Ethan
>
> > After an initial round of TLS refinement Refmac stops and and claims a
> > problem but nevertheless writes at the end "Task completed successfully"
> > and does not write any file despite it claims to have it done. I copied a
> > part of the log file at the end of the mail
> > Could anyone point me to the mistake i made probably?
> >
> >
> > Thanks in advance
> >
> > Christian
> >
> >
> > #CCP4I VERSION CCP4Interface 2.0.6
> > #CCP4I SCRIPT LOG refmac5
> > #CCP4I DATE 11 Oct 2010 17:37:30
> > #CCP4I USER roth
> > #CCP4I PROJECT sharpoutputrefinement
> > #CCP4I JOB_ID 19
> > #CCP4I SCRATCH /tmp
> > #CCP4I HOSTNAME bbzws339.bbz.uni-leipzig.de
> > #CCP4I PID 13018
> >
> > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
> > <html> <!-- CCP4 HTML LOGFILE -->
> > <hr>
> > <!--SUMMARY_END--></FONT></B>
> > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
> > <pre>
> >
> > ###############################################################
> > ###############################################################
> > ###############################################################
> > ### CCP4 6.1: Refmac_5.5.0109 version 5.5.0109 : 13/10/09##
> > ###############################################################
> > User: unknown Run date: 11/10/2010 Run time: 17:37:30
> >
> >
> > Please reference: Collaborative Computational Project, Number 4. 1994.
> > "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,
> > 760-763.
> > as well as any specific reference in the program write-up.
> >
> > <!--SUMMARY_END--></FONT></B>
> > $TEXT:Reference1: $$ comment $$
> > "Refinement of Macromolecular Structures by the Maximum-Likelihood
> > Method:" G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
> > Acta Crystallogr. D53, 240-255
> > EU Validation contract: BIO2CT-92-0524
> >
> > $$
> > $SUMMARY :Reference1: $$ Refmac: $$
> >
> > :TEXT:Reference1: $$
> >
> > Data line--- make check NONE
> > Data line--- make hydrogen ALL hout NO peptide NO
> > cispeptide NO ssbridge YES symmetry YES sugar YES
> > connectivity NO link NO
> > Data line--- refi type REST PHASE SCBL BBLU resi MLKF
> > meth CGMAT bref ISOT
> > Data line--- refi tlsc 10
> > Data line--- ncyc 25
> > Data line--- scal type SIMP LSSC ANISO EXPE
> > Data line--- solvent YES
> > Data line--- weight MATRIX 0.1
> > Data line--- monitor MEDIUM torsion 10.0 distance 10.0
> > angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere
> > 10.0 rbond 10.0 ncsr 10.0
> > Data line--- labin FP=FP SIGFP=SIGFP HLA=HLA HLB=HLB HLC=HLC HLD=HLD
> > FREE=FreeR_flag
> > Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT
> > PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
> > Data line--- PNAME sharpoutputrefinement
> > Data line--- DNAME hrsync
> > Data line--- RSIZE 80
> > Data line--- END
> >
> > OPENED INPUT MTZ FILE
> > Logical Name: HKLIN Filename:
> > /homes/roth/dlhdata/sharp/eden_unique.mtz
> >
> >
> > Spacegroup information obtained from library file:
> > Logical Name: SYMINFO Filename:
> > /software/linuxsoft/ccp4/ccp4-6.1.3/lib/data/syminfo.lib
> >
> >
> > **** Input and Default parameters# ****
> >
> >
> > Input coordinate file. Logical name - XYZIN actual file name -
> > /homes/roth/dlhdata/sharp/shrefmac9.pdb
> > Output coordinate file. Logical name - XYZOUT actual file name -
> > /homes/roth/dlhdata/sharp/shrefmac10.pdb
> > Input reflection file. Logical name - HKLIN actual file name -
> > /homes/roth/dlhdata/sharp/eden_unique.mtz
> > Output reflection file. Logical name - HKLOUT actual file name -
> > /homes/roth/dlhdata/sharp/eden_refmac3.mtz
> >
> > Cell from mtz : 61.560 69.500 133.350 90.000 90.000
> > 90.000 Space group from mtz: number - 19; name - P 21 21 21
> >
> > Refinement type : Restrained
> >
> >
> > ***TLS refinement cycle*** 2
> >
> > 1
> > 0.1153065 0.1254572 0.1168760 1.2506233E-02
> > 2.1331017E-03 1.5424690E-04
> > -1.4598943E-02 -3.3578421E-03 -1.7373050E-02 -3.3114674E-03
> > -1.3628958E-02 -2.4346421E-03
> > -8.4016532E-02 4.1347187E-02 -0.1191208 -0.1013065 -0.1222848
> > 0.1371335 -0.2420141 5.1373582E-02
> > -0.3787168
> > Problem
> > xyz 1107 48.64835 38.25826 83.76399 -34.85817
> > 8.685342 -6.930134 -12.26284 -18.79212 3.157892
> > 19.69073 -34.85817 0.6871372 23.66340 -0.3420097
> > -0.5949482 0.7273692
> > *************************************************************************
> >** * Information from CCP4Interface script
> > *************************************************************************
> >** Writing final coordinates (XYZOUT) to
> > /homes/roth/dlhdata/sharp/shrefmac10.pdb
> > *************************************************************************
> >**
> >
> > *************************************************************************
> >** * Information from CCP4Interface script
> > *************************************************************************
> >** Writing final phases (HKLOUT) to
> > /homes/roth/dlhdata/sharp/eden_refmac3.mtz
> > *************************************************************************
> >**
> >
> > *************************************************************************
> >** * Information from CCP4Interface script
> > *************************************************************************
> >** Writing final TLS (TLSOUT) to
> > /homes/roth/dlhdata/sharp/dlhtls_refmac1.tls
> > *************************************************************************
> >**
> >
> >
> > #CCP4I TERMINATION STATUS 1
> > #CCP4I TERMINATION TIME 11 Oct 2010 17:42:38
> > #CCP4I TERMINATION OUTPUT_FILES
> > /homes/roth/dlhdata/sharp/sharpoutputrefinement_19_hrsync.refmac.cif
> > sharpoutputrefinement
> > #CCP4I MESSAGE Task completed successfully
>
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