Focus alignment

Overview

When aligning binding sites, it's useful to focus on a particular subset of atoms. However, alignments can go haywire when choosing non-contiguous subsets of atoms. To get around this we first perform a sequence alignment to establish an initial pairing. Then, the user-specified sub-selection is used to pare down the equivalenced atoms for pair-fitting. See the examples.

Examples

focus_alignment 1cll, 1ggz, 1cll and i. 4-20

focus_alignment 2erk, 2b9f, 2erk and i. 50-75

• 

  global alignment of 1cll and 1ggz

• 

  focused alignment on residues 4-20 in 1cll on original atoms from global pairing; notice the white-colored residues are the focus of this alignment

The Code

# focus_alignment
#
# Author: Jason Vertrees
# Date  : 08-17-2011
#
import pymol

# example usage
# focus_alignment 2erk, 2b9f, i. 50-70 and 2erk
# focus_alignment 1cll, 1ggz, 1cll and i. 4-20

def focus_alignment(obj1, obj2, sel, debug=False):
    """
    PARAMS
      obj1
          structure 1

      obj2
          structure 2

      sel
          the selection from either obj1 or
          obj2 to focus the pair_fitting on.
          When providing this selection, please
          make sure you also specify selected
          atoms from ONE object.

    NOTES
    
    This function will first align obj1 and obj2 using
    a sequence alignment. This creates a mapping of
    residues from obj1 to obj2. Next, the selection, sel,
    is used to find only those atoms in the alignment and
    in sel. These atoms are paired with their mapped
    atoms from the alignment in the other object. These
    two subsets of atoms are then pair_fit to give
    an optimal sub-alignment.
    """

    aln = "aln"
    _sel = "__sel"
    ssel_model = ""
    a1, a2, a_target, modelA, modelB, sel_model = [],[],[],[],[],[]
    obj1, obj2 = "poly and " + obj1,  "poly and " + obj2

    # space dictionary for iterate
    space = { 'a1' : a1, 
              'a2' : a2,
              'a_target' : a_target, 
              'sel_model' : sel_model,
              'modelA' : modelA,
              'modelB' : modelB }

    # initial unfocused alignment
    cmd.align(obj1, obj2, cycles=0, object=aln)

    # record the initial indices
    s = "n. CA and (%s and %s)"
    cmd.iterate(s % (obj1,aln), "a1.append(index)",space=space)
    cmd.iterate(s % (obj2,aln), "a2.append(index)",space=space)

    if debug:
        print "# [debug] num atom in aln1 = ", len(a1)
        print "# [debug] num atom in aln2 = ", len(a2)

    # determine who owns the focused selection and
    # get canonical object names
    cmd.iterate("first %s" % sel, "sel_model.append(model)",space=space)
    cmd.iterate("first %s" % obj1, "modelA.append(model)",space=space)
    cmd.iterate("first %s" % obj2, "modelB.append(model)",space=space)
    ssel_model = sel_model[0]

    if debug:
        print "# [debug] selection is in object %s" % ssel_model

    # focus the target selection
    cmd.iterate(sel + " and n. CA", "a_target.append(index)",space=space)

    if debug:
        print "# [debug] a_target has %d members." % len(a_target)

    # select the correct object from which to index
    target_list = None
    if ssel_model==modelA[0]:
        target_list = a1
    elif sel_model==modelB[0]:
        target_list = a2
    else:
        print "# error: selection on which to focus was not found"
        print "# error: in either object passed in."
        print sel_model
        print modelA
        print modelB
        return False

    id1, id2 = [], []
    for x in a_target:
        try:
            idx = target_list.index(x)
            if debug:
                print "Current index: %d" % idx
            id1.append( str(a1[idx]) )
            id2.append( str(a2[idx]) )
        except:
            pass

    if debug: 
        print "# [debug] id1 = %s" % id1
        print "# [debug] id2 = %s" % id2
        
    sel1 = "+".join(id1)
    sel2 = "+".join(id2)
    
    if debug:
        print "# [debug] sel1 = %s" % sel1

    cmd.pair_fit(obj1 + " and aln and index " + sel1,
                 obj2 + " and aln and index " + sel2)

cmd.extend("focus_alignment", focus_alignment)
print " A new function 'focus_alignment' was added to PyMOL."
print " Type 'help focus_alignment' if you need help."