Yes, I've done this quite a few times since it came out. Amazing how
quick it can be to search the whole PDB. Less than 8 hours on some of
my boxes.
You probably have to run the simbad-database program? Used to be you
had to download morda separately, but now it seems automatic. Only
problem is you need to be root or some other user who can write to the
CCP4 installation directory.
# as root:
source /programs/ccp4-7.0/bin/ccp4.setup-csh
simbad-database lattice
simbad-database morda
However, I should admit that now that I try to run it again it seems to
be broken. Doesn't seem to be a way to point simbad to the new-style
copy of the database. However, if I point it to the one I made in 2018
it works fine:
simbad-morda ./data.mtz -nproc 448 -morda_db ${CCP4}/simbad-morda-db
But if I run:
simbad-morda ./data.mtz
it crashes after ~90 s with:
SIMBAD EXITING AT...
Traceback (most recent call last):
File
"/home/programs/ccp4-7.0/lib/py2/simbad/command_line/simbad_morda.py",
line 91, in
main()
File
"/home/programs/ccp4-7.0/lib/py2/simbad/command_line/simbad_morda.py",
line 66, in main
solution_found = simbad.command_line._simbad_morda_search(args)
File
"/home/programs/ccp4-7.0/lib/py2/simbad/command_line/__init__.py", line
456, in _simbad_morda_search
chunk_size=args.chunk_size
File
"/home/programs/ccp4-7.0/lib/py2/simbad/rotsearch/amore_search.py", line
194, in run
pdb_struct.from_file(dat_model)
File "/home/programs/ccp4-7.0/lib/py2/simbad/util/pdb_util.py", line
36, in from_file
self.assert_hierarchy()
File "/home/programs/ccp4-7.0/lib/py2/simbad/util/pdb_util.py", line
57, in assert_hierarchy
assert len(self.hierarchy.models()) > 0, 'No models found in hierarchy'
AssertionError: No models found in hierarchy
Ronan?
-James Holton
MAD Scientist
On 7/25/2020 3:55 PM, Peat, Tom (Manufacturing, Parkville) wrote:
Hello All,
I would like to run SIMBAD to do a brute force MR on a data set that I
have (running Contra-Miner didn't come up with any known contaminants
and running SIMBAD with the Lattice and Contaminants search didn't
give me anything).
As I understand the documentation, SIMBAD can be run using the MORDA
database (which I have on my computer).
I've managed to run SIMBAD doing the Lattice and Contaminants search,
but haven't managed to get it to run using the MORDA database for the
brute force MR.
As far as I can tell, the servers only run the L & C and not the brute
force MR.
Does anyone have experience (hopefully positive) doing this brute
force MR?
cheers, tom
Tom Peat
Proteins Group
Biomedical Program, CSIRO
343 Royal Parade
Parkville, VIC, 3052
+613 9662 7304
+614 57 539 419
tom.p...@csiro.au
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