Dear IMP,
I'm trying to figure out how one would use the IDEAL_HELIX representation
for purposes of EMRestraint.
I'm working with the tutorial example and the representation looks like
this:
m = IMP.Model()
representation = IMP.pmi.representation.Representation(m,upperharmonic=True,
disorderedlength=False)
# compname hier_name color fastafile
fastaid pdbname chain resrange read
beadsize rigid_body super_rigid_body emnum_components, emtxtfilename
emmrcfilename
domains=[("Rpb1", "Rpb1_1", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:A", datadir+"1WCM_map_fitted.pdb", "A", (1,1140,0), True,
20, None, None, 57, None, None, None),
("Rpb1", "Rpb1_2", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:A", datadir+"1WCM_map_fitted.pdb", "A", (1141,1274,0), True,
20, None, None, 7, None, None, None),
("Rpb1", "Rpb1_3", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:A", datadir+"1WCM_map_fitted.pdb", "A", (1275,1455,0), True,
20, None, None, 9, None, None, None),
("Rpb2", "Rpb2_1", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:B", datadir+"1WCM_map_fitted.pdb", "B", (1,1102,0), True,
20, None, None, 55, None, None, None),
("Rpb2", "Rpb2_2", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:B", datadir+"1WCM_map_fitted.pdb", "B", (1103,-1,0), True,
20, None, None, 6, None, None, None),
("Rpb3", "Rpb3", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:C", datadir+"1WCM_map_fitted.pdb", "C", (1,-1,0), True,
20, None, None, 16, None, None, None),
("Rpb4", "Rpb4_1", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:D", "BEADS", None, (1,54,0), True,
20, 1, [1], 0, None, None, [1]),
("Rpb4", "Rpb4_2", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:D", "IDEAL_HELIX", None, (55,75,0), True,
1, 1, [1], 20, None, None, [1]),
("Rpb4", "Rpb4_3", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:D", "BEADS", None, (76,-1,0), True,
20, 1, [1], 0, None, None, [1]),
("Rpb5", "Rpb5", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:E", datadir+"1WCM_map_fitted.pdb", "E", (1,-1,0), True,
20, None, None, 11, None, None, None),
("Rpb6", "Rpb6", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:F", datadir+"1WCM_map_fitted.pdb", "F", (1,-1,0), True,
20, None, None, 8, None, None, None),
("Rpb7", "Rpb7", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:G", "BEADS", None, (1,-1,0), True,
20, 4, [4], 0, None, None, [4]),
("Rpb8", "Rpb8", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:H", datadir+"1WCM_map_fitted.pdb", "H", (1,-1,0), True,
20, None, None, 7, None, None, None),
("Rpb9", "Rpb9", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:I", datadir+"1WCM_map_fitted.pdb", "I", (1,-1,0), True,
20, None, None, 6, None, None, None),
("Rpb10", "Rpb10", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:J", datadir+"1WCM_map_fitted.pdb", "J", (1,-1,0), True,
20, None, None, 4, None, None, None),
("Rpb11", "Rpb11", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:K", datadir+"1WCM_map_fitted.pdb", "K", (1,-1,0), True,
20, None, None, 6, None, None, None),
("Rpb12", "Rpb12", 0.00, datadir+"1WCM_new.fasta.txt",
"1WCM:L", datadir+"1WCM_map_fitted.pdb", "L", (1,-1,0), True,
20, None, None, 4, None, None, None)]
bm1 = IMP.pmi.macros.BuildModel1(representation)
bm1.build_model(domains)
When I was modeling Rpb4 and Rpb7 as BEADS, everything seemed to be
working. I then tried modeling a stretch of Rpb4 as IDEAL_HELIX, but I'm
not sure the density of that helix is recognized and the
representation/density doesn't look they way I would expect in Chimera. I
thought I should have it represented by 1 bead/aa. I basically just want
to model it as a straight tube both for representational and EM density
purposes.
Thanks much,
Julian
