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# this script uses the alignment engine to match aligned C-alpha atoms
# in related structures and graft a selection from one to the other
# load structures
fetch 1t46 1oky, async=0
as ribbon
# specify mobile and target objects / atoms
select mobile, 1t46////CA
select target, 1oky////CA
# specify the input selection to match across the alignment
select match_inp, 1oky///86-91/CA
##### generic from here down #####
# initialize the output selection
select match_out, none
# perform the alignment
align mobile, target, object=aln
python
# work around indexing bug in pre-1.2 versions
if cmd.get_version()[1]<1.2:
fixver = 1
else:
fixver = 0
# get raw alignment from Python
aln_list=cmd.get_raw_alignment("aln")
# iterate through matching atom sets
for match in aln_list:
# init. temporary selections for accumulating matched atoms
cmd.select("tmp_mob","none")
cmd.select("tmp_tgt","none")
# find corresponding atoms in mobile & target selectionsw
for atom in match:
atom_sele = "%s`%d"%(atom[0], atom[1]+fixver)
cmd.select("tmp_mob","tmp_mob or (mobile and %s)"%atom_sele)
cmd.select("tmp_tgt","tmp_tgt or (target and %s)"%atom_sele)
# when both are found, match from input selection to output selection
if (cmd.count_atoms("tmp_mob")==1) and (cmd.count_atoms("tmp_tgt")==1):
if cmd.count_atoms("tmp_mob and match_inp"):
cmd.select("match_out","match_out or tmp_tgt")
elif cmd.count_atoms("tmp_tgt and match_inp"):
cmd.select("match_out","match_out or tmp_mob")
python end
deselect
enable match_out
orient match_out
zoom match_out, 3
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