Thanks Gabor, this is now cooking away nicely. At least, it's running...
Best wishes,
Graeme
On 17 February 2012 12:32, Dr G. Bunkoczi
Hi Graeme,
unfortunately, command line arguments and multiple scopes do not match very well, so you need to use a properly formatted PHIL instead for the composition (this could also be read from stdin with the --stdin switch in case you prefer not to write temporary files):
composition { count = 3 component { sequence = sequence.pir search { services = local ncbi max_hits = 3 } } }
I would also strongly discourage mode=full in this case, as it may lead to a combinatorial explosion, especially with a large number of models. You may also want to use "template_equivalence=True" to reduce the calculation demand.
You could also allocate more CPUs if you have in your box or if the cluster is supported. If using a cluster, set packing_pool to a larger number, e.g. 40 or 100 (this depends on the job startup overhead), and allocate only as many CPUs as you are expecting to be available (i.e. free).
HTH, Gabor
On Feb 17 2012, Graeme Winter wrote:
Hi Folks,
Following from the newsletter article I am trying to test out phaser.MRage. I have a well solved case which I know is in the pdb and a sequence file:
phaser.MRage hklin=data.mtz composition.component.sequence=sequence.pir symmetry_exploration=pointgroup mode=full search.services=ncbi composition.count=3
however it generates a second component then complains it knows nothing about this:
Sorry: Molecular weight needed for component 2.
Any suggestions how to get around this?
Many thanks,
Graeme
[gw56@ws050 rage]$ phaser.MRage hklin=data.mtz composition.component.sequence=sequence.pir symmetry_exploration=pointgroup mode=full search.services=ncbi composition.count=3 ############################################################################### # MRage version 0.1.0 # ###############################################################################
All configuration options: --------------------------
hklin = data.mtz labin = None resolution_cutoff = 2.5 crystal_symmetry { unit_cell = None space_group = None } mode = quick *full symmetry_exploration = *pointgroup enantiomorph dataset output { root = "mrage" max_solutions_to_write = 0 gui_base_dir = None save_aniso_data = False job_title = None } composition { count = 3 component { sequence = sequence.pir stoichiometry = 1 ensemble { coordinates { pdb = None identity = None } } model_collection { trim = False coordinates { pdb = None identity = None } } template { pdb = None alignment = None } homology { file_name = None max_hits = 3 } search { services = local ncbi max_hits = 3 } } component { sequence = None stoichiometry = 1 ensemble { coordinates { pdb = None identity = None } } model_collection { trim = False coordinates { pdb = None identity = None } } template { pdb = None alignment = None } homology { file_name = None max_hits = 3 } search { services = local *ncbi max_hits = 3 } } } queue { technology = lsf threading sge *multiprocessing pbs cpus = 1 submission_command = None qslot_cpus = 1 } packing_pool = 20 rotation_peaks_cutoff = 0.75 post_refinement_cutoff = 0.75 final_selection_cutoff = 0.75 b_factor_refinement = True significant_peak_threshold = 7.0 sculptor_protocols = 11 10 13 12 1 3 2 5 4 7 6 9 8 *all minimal template_equivalence = False exclude_pdb_ids = None simple_run { enable = False component_sequence = None template_model = None blast_services = local ncbi max_blast_hits = 3 }
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