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 >
