This looks like it is my fault. This is only a guess, but I suspect it is
running the "wrong" python.
I don't have /sw/share/xtal/ccp4-6.0/bin/mrbump. I'll try to mess around
with it this weekend.
Meanwhile, if you would be willing to conduct the following experiment
for me and tell me if anything works, I would be grateful:
Figure out where python -u /sw/share/xtal/ccp4-6.0/bin/mrbump is being
invoked, and change it to either /usr/bin/python or /sw/bin/python. I am
going to predict the first one is the one you need, but I really don't
know.
Sorry this isn't more helpful.
Bill
On Fri, 28 Jul 2006, Kendall Nettles wrote:
I encountered a crash when using MR Bump. As a test, I re-ran a job that had
worked successfully, and had the same crash. Any suggestions?
--
Kendall W. Nettles, PhD
Assistant Professor
Department of Biochemistry
The Scripps Research Institute
5353 Parkside Dr.?
Jupiter Fl 33458
office 561-799-8851
fax 561-799-8957
cell 561-306-7566
Search log message: Number of valid PDB matches found in searches = 270
***************************************************************************
* Information from CCP4Interface script
***************************************************************************
The program run with command: python -u /sw/share/xtal/ccp4-6.0/bin/mrbump
HKLIN /shyamala_CD/un-liganded/P43212_noligand.mtz SEQIN
/shyamala_CD/un-liganded/hER.txt HKLOUT
/shyamala_CD/un-liganded/P43212_noligand_mrbump_soln1.mtz XYZOUT
/shyamala_CD/un-liganded/P43212_noligand_mrbump_soln1.pdb
has failed with error message
Traceback (most recent call last):
File "/sw/share/xtal/ccp4-6.0/bin/mrbump", line 53, in ?
master.fast_search_MR(init)
File
"/sw/share/xtal/ccp4-6.0/src/mrbump/include/initialisation/MRBUMP_master.py"
, line 133, in fast_search_MR
ps.alignment(mstat.chain_list.keys(), target_info, init, mstat)
File "/sw/share/xtal/ccp4-6.0/src/mrbump/include/structures/Matches.py",
line 922, in alignment
align.score(list, mstat, mstat.all_raw_file, mstat.all_align_file,
'clustalw')
File
"/sw/share/xtal/ccp4-6.0/src/mrbump/include/seq_align/Align_score.py", line
63, in score
s.write_align_files(list, mstat)
File "/sw/share/xtal/ccp4-6.0/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: '2ewp_B'
***************************************************************************
#CCP4I TERMINATION STATUS 0 "Traceback (most recent call last): File
"/sw/share/xtal/ccp4-6.0/bin/mrbump", line 53, in ?
master.fast_search_MR(init) File
"/sw/share/xtal/ccp4-6.0/src/mrbump/include/initialisation/MRBUMP_master.py"
, line 133, in fast_search_MR ps.alignment(mstat.chain_list.keys(),
target_info, init, mstat) File
"/sw/share/xtal/ccp4-6.0/src/mrbump/include/structures/Matches.py", line
922, in alignment align.score(list, mstat, mstat.all_raw_file,
mstat.all_align_file, 'clustalw') File
"/sw/share/xtal/ccp4-6.0/src/mrbump/include/seq_align/Align_score.py", line
63, in score s.write_align_files(list, mstat) File
"/sw/share/xtal/ccp4-6.0/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:
'2ewp_B'"
#CCP4I TERMINATION TIME 28 Jul 2006 14:03:50
#CCP4I MESSAGE Task failed
