Macro AA_CDR_Arrange

The AHo numbering scheme specifies that sequence gaps should be centered around the turn position in the longest sequence variant, or centered between corresponding positions in neighboring beta-strands. The macro AA_CDR_arrange helps to align sequences in this manner, since it coalesces all gaps in a selected sequence block in the center of this block:

Usage:

Sub AA_CDR_Arrange()

'Counts number of valid amino acid within selected rows
'Consolidates gaps and places them in the center of the sequence block

    If Selection.Columns.Count = 0 Then      'Error, nothing selected
        MsgBox Prompt:="No cells selected, please select the sequences you wish to color"
        Exit Sub
    End If

'get extent of current selection
    i1 = Selection.Row
    i2 = i1 + Selection.Rows.Count - 1
    j1 = Selection.Column
    j2 = j1 + Selection.Columns.Count - 1
   
    For i = i1 To i2 Step 1
        a = 0
        b = 0
        For j = j2 To j1 Step -1
           If (Cells(i, j) = "" Or Cells(i, j) = " ") Then
               Cells(i, j) = "."
          End If
          If (Cells(i, j) = ".") Then
                Cells(i, j).Select
                Selection.Delete Shift:=xlToLeft
                a = a + 1
                Else
                b = b + 1
          End If
        Next j

        If Not (a = 0) Then
            Range(Cells(i, j1 + Int((b + 0.99) / 2)), Cells(i, j2 - Int((b - 1) / 2) - 1)).Select
            Selection.Insert Shift:=xlToRight
        End If
       
    Next i

    Range(Cells(i1,j1), Cells(i2,j2)).Select

End Sub