Dear CCP4 programmers,
I am getting crashes in Buccaneer when I try to extend a current model, and
have the options on either of "specify atoms from initial model" or "specify
heavy atom/MR model". In my case, these are sort of important options, since
the model needs to have calcium atoms in it to work. Or maybe Buccaneer can't
deal with calcium or other non-protein atoms? Just guessing here. I've pasted
the log file below.
All the best,
Jacob Keller
#CCP4I VERSION CCP4Interface 6.5.003
#CCP4I SCRIPT LOG buccaneer_pipeline
#CCP4I DATE 15 Feb 2015 14:31:32
#CCP4I USER 'UNKNOWN'
#CCP4I PROJECT P32
#CCP4I JOB_ID 99
#CCP4I SCRATCH C:/ccp4temp/
#CCP4I HOSTNAME KELLERJ-LW1
#CCP4I PID 4544
################################################################
### buccaneer-pipeline v1.5 ###
################################################################
---------------------- INPUT PARAMETERS ----------------------
title [No title given]
pdbin-ref C:/CCP4/6.5/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref C:/CCP4/6.5/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin F:/SLC26/campepA33xtal/SteveCaMpepA3.seq
mtzin F:/SLC26/campepA33xtal/P32/PROCESSING/P32_96_parrot.mtz
colin-fo FP,SIGFP
colin-free FreeR_flag
colin-hl parrot.ABCD.A,parrot.ABCD.B,parrot.ABCD.C,parrot.ABCD.D
pdbin F:/SLC26/campepA33xtal/P32/REFINEMENT/KellerBuild03.pdb
pdbin-sequence-prior F:/SLC26/campepA33xtal/P32/REFINEMENT/KellerBuild03.pdb
pdbout F:/SLC26/campepA33xtal/P32/PROCESSING/P32_96_parrot_buccaneer1.pdb
cycles 5
buccaneer-anisotropy-correction
buccaneer-fix-position
buccaneer-fast
buccaneer-1st-cycles 3
buccaneer-1st-sequence-reliability 0.99
buccaneer-1st-correlation-mode
buccaneer-nth-cycles 2
buccaneer-nth-sequence-reliability 0.99
buccaneer-nth-correlation-mode
buccaneer-new-residue-name UNK
buccaneer-resolution 2.0
buccaneer-keyword model-filter-sigma 3.0
buccaneer-keyword mr-model-filter-sigma 3.0
refmac-mlhl 1
refmac-twin 1
prefix F:/SLC26/campepA33xtal/P32/PROCESSING/99_buccaneer_pipeline/
---------------------- DEFAULT PARAMETERS ----------------------
----------------------------------------------------------------
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<pre>
###############################################################
###############################################################
###############################################################
### CCP4 6.5.003: cbuccaneer version 1.6.0 : 25/02/14##
###############################################################
User: kellerj Run date: 15/ 2/2015 Run time: 14:31:32
Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67,
235-242.
as well as any specific reference in the program write-up.
Copyright 2002-2010 Kevin Cowtan and University of York.
$TEXT:Reference: $$ Please reference $$
'Fitting molecular fragments into electron density'
Cowtan K. (2008) Acta Cryst. D64, 83-89.
$$
$TEXT:Reference: $$ Please reference $$
'The Buccaneer software for automated model building'
Cowtan K. (2006) Acta Cryst. D62, 1002-1011.
$$
title [No title given]
pdbin-ref C:/CCP4/6.5/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref C:/CCP4/6.5/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin F:/SLC26/campepA33xtal/SteveCaMpepA3.seq
mtzin F:/SLC26/campepA33xtal/P32/PROCESSING/P32_96_parrot.mtz
colin-fo FP,SIGFP
colin-hl parrot.ABCD.A,parrot.ABCD.B,parrot.ABCD.C,parrot.ABCD.D
colin-free FreeR_flag
pdbin F:/SLC26/campepA33xtal/P32/REFINEMENT/KellerBuild03.pdb
pdbin-sequence-prior F:/SLC26/campepA33xtal/P32/REFINEMENT/KellerBuild03.pdb
pdbout F:/SLC26/campepA33xtal/P32/PROCESSING/99_buccaneer_pipeline/build.pdb
anisotropy-correction
fix-position
fast
cycles 3
sequence-reliability 0.99
correlation-mode
new-residue-name UNK
resolution 2.0
model-filter-sigma 3.0
mr-model-filter-sigma 3.0
Correlation mode selected
MTZ file: F:/SLC26/campepA33xtal/P32/PROCESSING/P32_96_parrot.mtz
Number of reflections: 166115 Number of columns: 44
Applying anisotropy correction:
| 0,-2.702e-019,-5.688e-016|
|-2.702e-019,-2.393e-013,-5.188e-018|
|-5.688e-016,-5.188e-018, -0.01335|
PDB file: F:/SLC26/campepA33xtal/P32/REFINEMENT/KellerBuild03.pdb
Number of atoms read: 9872
PDB file: F:/SLC26/campepA33xtal/P32/REFINEMENT/KellerBuild03.pdb
Number of atoms read: 9872
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: C:/CCP4/6.5/bin/ccp4-python.bat -u
C:/CCP4/6.5/bin/buccaneer_pipeline -stdin
has failed with error message
cbuccaneer -stdin
title [No title given]
pdbin-ref C:/CCP4/6.5/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref C:/CCP4/6.5/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin F:/SLC26/campepA33xtal/SteveCaMpepA3.seq
mtzin F:/SLC26/campepA33xtal/P32/PROCESSING/P32_96_parrot.mtz
colin-fo FP,SIGFP
colin-hl parrot.ABCD.A,parrot.ABCD.B,parrot.ABCD.C,parrot.ABCD.D
colin-free FreeR_flag
pdbin F:/SLC26/campepA33xtal/P32/REFINEMENT/KellerBuild03.pdb
pdbin-sequence-prior F:/SLC26/campepA33xtal/P32/REFINEMENT/KellerBuild03.pdb
pdbout F:/SLC26/campepA33xtal/P32/PROCESSING/99_buccaneer_pipeline/build.pdb
anisotropy-correction
fix-position
fast
cycles 3
sequence-reliability 0.99
correlation-mode
new-residue-name UNK
resolution 2.0
model-filter-sigma 3.0
mr-model-filter-sigma 3.0
Traceback (most recent call last):
File "C:/CCP4/6.5/bin/buccaneer_pipeline", line 198, in <module>
control.run_program_template( buccaneer_1st )
File "C:\CCP4\6.5\lib\py2\CCP4pipeline.py", line 740, in run_program_template
self.run_program( prgm, argx, cmdx )
File "C:\CCP4\6.5\lib\py2\CCP4pipeline.py", line 729, in run_program
raise( StandardError( 'Fail in program <'+prgm+'>' ) )
StandardError: Fail in program <cbuccaneer>
***************************************************************************
#CCP4I TERMINATION STATUS 0 "cbuccaneer -stdin title [No title given]
pdbin-ref C:/CCP4/6.5/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref C:/CCP4/6.5/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo FP.F_sigF.F,FP.F_sigF.sigF colin-ref-hl
FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D seqin
F:/SLC26/campepA33xtal/SteveCaMpepA3.seq mtzin
F:/SLC26/campepA33xtal/P32/PROCESSING/P32_96_parrot.mtz colin-fo FP,SIGFP
colin-hl parrot.ABCD.A,parrot.ABCD.B,parrot.ABCD.C,parrot.ABCD.D
colin-free FreeR_flag pdbin
F:/SLC26/campepA33xtal/P32/REFINEMENT/KellerBuild03.pdb pdbin-sequence-prior
F:/SLC26/campepA33xtal/P32/REFINEMENT/KellerBuild03.pdb pdbout
F:/SLC26/campepA33xtal/P32/PROCESSING/99_buccaneer_pipeline/build.pdb
anisotropy-correction fix-position fast cycles 3 sequence-reliability 0.99
correlation-mode new-residue-name UNK resolution 2.0 model-filter-sigma
3.0 mr-model-filter-sigma 3.0 Traceback (most recent call last): File
"C:/CCP4/6.5/bin/buccaneer_pipeline", line 198, in <module>
control.run_program_template( buccaneer_1st ) File
"C:\CCP4\6.5\lib\py2\CCP4pipeline.py", line 740, in run_program_template
self.run_program( prgm, argx, cmdx ) File
"C:\CCP4\6.5\lib\py2\CCP4pipeline.py", line 729, in run_program raise(
StandardError( 'Fail in program <'+prgm+'>' ) ) StandardError: Fail in program
<cbuccaneer>"
#CCP4I TERMINATION TIME 15 Feb 2015 14:31:37
#CCP4I TERMINATION OUTPUT_FILES
F:/SLC26/campepA33xtal/P32/PROCESSING/99_buccaneer_pipeline/
#CCP4I MESSAGE Task failed
*******************************************
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
*******************************************
