*** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk ***
Dear Francisco, Sorry to hear that you are having trouble with mrbump. The error you have encountered should be fixed in the latest version of mrbump (0.3.1) which is available to download from www.ccp4.ac.uk/MrBUMP. Regards, Ronan ######################################################################### Ronan Keegan email: [EMAIL PROTECTED] e-HTPX/CCP4 phone: (+)44-1925-603701 C18, Daresbury Laboratory fax: (+)44-1925-603825 Warrington WA4 4AD UK ######################################################################### On Thu, 15 Jun 2006 [EMAIL PROTECTED] wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Dear All : > > When I try to run MrBump in my system I always get this fancy error (you > can see the log pasted at the end of the message). Any suggestions what to > do ??. Many thanks. > > Cheers > > Francisco > > > > My system : Linux > My distro : Mandriva 2006 > I am behind a firewall > I am using a proxy > > > -------------------------------- > #CCP4I VERSION CCP4Interface 1.4.4.1 > #CCP4I SCRIPT LOG mrbump > #CCP4I DATE 15 Jun 2006 17:21:25 > #CCP4I USER fenguita > #CCP4I PROJECT kpn30_id14 > #CCP4I JOB_ID 34 > #CCP4I SCRATCH /home/fenguita/tmp > #CCP4I HOSTNAME clark > #CCP4I PID 18547 > > > ####################################################################### > ####################################################################### > ####################################################################### > # CCP4: MRBUMP - Automated Bulk Molecular Replacement (version 0.3) # > ####################################################################### > > Version date: Wed Apr 19 18:29:38 2006 > > ENTER KEYWORD INPUT FROM FILE OR FROM STANDARD INPUT > --> > Only generate models set to: False > --> > > column F labelled as F_native > column SIGF labelled as SIGF_native > column FREER_FLAG labelled as FreeR_flag > > --> > Job identifier: 34 > --> > Root directory: /home/fenguita/work/kpn30/id14-4/x2/process > --> > Results HTML location: > /home/fenguita/work/kpn30/id14-4/x2/process/results_34.html > --> > Number of search models to use in MR: 10 > --> > Number of models to use in Phaser ensemble: 5 > --> > Default MR program: PHASER > --> > Default sequence alignment program: MAFFT > --> > Debug set to: False > --> > SCOP search set to: True > --> > SSM search set to: False > --> > PQS search set to: True > --> > Generate PDBClip models set to: True > --> > Generate Molrep models set to: True > --> > Generate Chainsaw models set to: True > --> > Generate Polyalanine models set to: False > --> > Run local Fasta search set to: False > --> > Update database files set to: True > --> > E value to use in fasta search: 0.030000 > --> > Number of clashes tolerated in Phaser: 5 > --> > Number of cycles of restrained refinement to use in Refmac: 30 > --> > No value given for NMASU. Number of molecules will be calculated > automatically > --> > List of PDB codes to ignore in the search: [] > --> > List of PDB codes to include in the search: [] > --> > Run in ISOLATED mode set to: False > --> > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > A newer version of MrBUMP is available (version 0.3.1) > This can be downloaded from: > http://www.ccp4.ac.uk/martyn/BMP/release/mrbump-0.3.1.tar.gz > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > > ************************************************************************************************ > Mode of operation: FULLMR - Search models will be created and used in > Molecaular Replacement. > ************************************************************************************************ > > Input MTZ file: > /home/fenguita/work/kpn30/id14-4/x2/process/kpn30_esrf_1.1.mtz > Input Sequence file: /home/fenguita/work/kpn30/id14-4/x2/process/kpn30.seq > Output MTZ file: > /home/fenguita/work/kpn30/id14-4/x2/process/kpn30_esrf_1.1_mrbump_soln1.mtz > Output PDB file: > /home/fenguita/work/kpn30/id14-4/x2/process/kpn30_esrf_1.1_mrbump_soln1.pdb > > > Database update: Checking the web to see if newer versions of the search > databases exist. > Database update: Fasta DB is up to date. > > Database update: Your PQS List DB file is out of date, attempting an > update... > Download error: Cannot retrieve new version of PQS List DB. Will use old > version > > Database update: Your PQS ASAList DB file is out of date, attempting an > update... > Download error: Cannot retrieve new version of PQS ASAList DB. Will use > old version > > Database update: Your PQS BIOList DB file is out of date, attempting an > update... > Download error: Cannot retrieve new version of PQS BIOList DB. Will use > old version > Database update: SCOP List DB is up to date. > > ################################### > ### Target Information ### > ################################### > > > > Matthews_Coef message: Estimated number of molecules: 6 > Matthews_Coef message: Score for this number of molecules: 0.460 > Matthews_Coef message: Actual Vm: 2.340 and Solvent content: 47.580 % > > > Sequence file: > /home/fenguita/work/kpn30/id14-4/x2/process/search_34/input/kpn30.seq > Reflection (MTZ) file: > /home/fenguita/work/kpn30/id14-4/x2/process/search_34/input/kpn30_esrf_1.1.mtz > Number of residues: 211 > Molecular Weight (daltons): 23244.390 > Number of molecules in a.s.u.: 6 > Resolution of collected data (angstroms): 3.200 > > > > ################################### > ### Fasta search ### > ################################### > > Fasta log message: e value used in Fasta search: 0.0300 > Fasta log message: Performing Fasta search using OCA service > > Fasta log message: Number of valid Fasta matches: 36 > > --------------------------------------------------------- > Fasta: Getting Template Sequences and Multiple Alignment: > --------------------------------------------------------- > > Search log message: Number of valid PDB matches found in searches = 22 > > *************************************************************************** > * Information from CCP4Interface script > *************************************************************************** > The program run with command: python -u > /usr/local/ccp4-6.0.1/ccp4-6.0.1/bin/mrbump HKLIN > /home/fenguita/work/kpn30/id14-4/x2/process/kpn30_esrf_1.1.mtz SEQIN > /home/fenguita/work/kpn30/id14-4/x2/process/kpn30.seq HKLOUT > /home/fenguita/work/kpn30/id14-4/x2/process/kpn30_esrf_1.1_mrbump_soln1.mtz > XYZOUT > /home/fenguita/work/kpn30/id14-4/x2/process/kpn30_esrf_1.1_mrbump_soln1.pdb > has failed with error message > > > Strategy: > NW-NS-i (Accurate but slow) > Iterative refinement method (max. 1000 iterations) > > Type '/usr/bin/mafft --help' for other options. > --memsave is for beta testing > > Traceback (most recent call last): > File "/usr/local/ccp4-6.0.1/ccp4-6.0.1/bin/mrbump", line 53, in ? > master.fast_search_MR(init) > File > "/usr/local/ccp4-6.0.1/ccp4-6.0.1/src/mrbump/include/initialisation/MRBUMP_master.py", > line 133, in fast_search_MR > ps.alignment(mstat.chain_list.keys(), target_info, init, mstat) > File > "/usr/local/ccp4-6.0.1/ccp4-6.0.1/src/mrbump/include/structures/Matches.py", > line 917, in alignment > align.score(list, mstat, mstat.all_raw_file, mstat.all_align_file, > 'mafft') > File > "/usr/local/ccp4-6.0.1/ccp4-6.0.1/src/mrbump/include/seq_align/Align_score.py", > line 63, in score > s.write_align_files(list, mstat) > File > "/usr/local/ccp4-6.0.1/ccp4-6.0.1/src/mrbump/include/seq_align/seperate.py", > line 89, in write_align_files > outfile=open(mstat.chain_list[chain].alignment.in_fasta_file, 'w') > KeyError: '2esf_B' > *************************************************************************** > > > #CCP4I TERMINATION STATUS 0 " Strategy: NW-NS-i (Accurate but slow) > Iterative refinement method (max. 1000 iterations) Type '/usr/bin/mafft > --help' for other options. --memsave is for beta testing Traceback (most > recent call last): File "/usr/local/ccp4-6.0.1/ccp4-6.0.1/bin/mrbump", > line 53, in ? master.fast_search_MR(init) File > "/usr/local/ccp4-6.0.1/ccp4-6.0.1/src/mrbump/include/initialisation/MRBUMP_master.py", > line 133, in fast_search_MR ps.alignment(mstat.chain_list.keys(), > target_info, init, mstat) File > "/usr/local/ccp4-6.0.1/ccp4-6.0.1/src/mrbump/include/structures/Matches.py", > line 917, in alignment align.score(list, mstat, mstat.all_raw_file, > mstat.all_align_file, 'mafft') File > "/usr/local/ccp4-6.0.1/ccp4-6.0.1/src/mrbump/include/seq_align/Align_score.py", > line 63, in score s.write_align_files(list, mstat) File > "/usr/local/ccp4-6.0.1/ccp4-6.0.1/src/mrbump/include/seq_align/seperate.py", > line 89, in write_align_files > outfile=open(mstat.chain_list[chain].alignment.in_fasta_file, 'w') > KeyError: '2esf_B'" > #CCP4I TERMINATION TIME 15 Jun 2006 17:21:42 > #CCP4I MESSAGE Task failed > > > > > > > > ----------------------------------------- > Francisco J. Enguita, Ph.D. > Host-pathogen Interactions Group > Macromolecular Crystallography Laboratory > ITQB > EAN, Av. da Rep?blica > 2781-901 Oeiras > Portugal > Phone : +351-21-4469663 > Fax : +351-21-4433644 > E-mail : [EMAIL PROTECTED] > ----------------------------------------- > >
