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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 República 2781-901 Oeiras Portugal Phone : +351-21-4469663 Fax : +351-21-4433644 E-mail : [EMAIL PROTECTED] -----------------------------------------
