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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]
-----------------------------------------
