Hello,
I am modeling a multistate system in PMI using
CrossLinkingMassSpectrometryRestraint in imp-2.15, and trying to
adapt imp-sampcon for the purpose.
I set up my system with 2 states having identical components with:
topology = IMP.pmi.topology.TopologyReader(topology_file,
fasta_dir=datadirectory,
pdb_dir=datadirectory)
topology2 = IMP.pmi.topology.TopologyReader(topology_file,
fasta_dir=datadirectory,
pdb_dir=datadirectory)
bm = IMP.pmi.macros.BuildSystem(m)
bm.add_state(topology)
bm.add_state(topology2)
root_hierarchy, dof = bm.execute_macro(max_rb_trans=rb_max_trans,
max_rb_rot=rb_max_rot,
max_bead_trans=bead_max_trans)
and later set up crosslinking restraint (after creating crosslink database) by:
cl_dsso = IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint(root_hier=root_hierarchy,
database=cldb2,
length=21.0,
slope=0.01,
resolution=1.0,
filelabel='dsso',
label="dsso",
linker=ihm.cross_linkers.dsso,
weight=1)
After running replica exchange, i am trying to extract distances for
my crosslinks (in theory 2 per protein copy, one in state 0 and one in
state 1).
However, when I for example extract distances from the stat file by
stat_file=IMP.pmi.output.ProcessOutput('rmfs/0.rmf3')
#extract distances for a specific crosslink restraint
stat_file.get_fields(['CrossLinkingMassSpectrometryRestraint_Distance_|dsso|1278.1|Protein1|148|Protein2|689|1|PSI|'])
I get a single distance per frame, corresponding to the distance in
the latest state to be added, not to the shortest distance in the
ensemble, and not one distance per state, as would make sense for
analysing crosslink violations. As far as I can tell the score is
behaving correctly overall (optimising for one state to be below the
cutoff).
I can still successfully run the first part of sampcon using score
cutoffs rather than distances. But I wonder if it is possible to
extract the shortest distance for each crosslink? Have I set up the
multistate system incorrectly?
(I am trying to work out how to set up the alignment etc for rmsd in
such a case, but I have a long way to go there.)
I can provide a test case if needed.
Many thanks in advance,
Andrea
