Align3dPlugin - Geneious 3d protein alignment plugin


I have created a Java 3d alignment plugin for Geneious 2.5.3--3.0.3. In Genious, you can select two PDB files (e.g. 1LYZ and 2LZM) and a 1d alignment made from them, and then choose the 'Align 3d structures' menu item or tool button. The 2 structures will be aligned using the alignment sequences, and the result returned as another PDB document.

In addition, diagnostic information will be printed out on the console:

If the Dali optimized 1d alignment sequence is used, it results in an RMSD error of 5.485784 rather than 15.501737 for the default Needleman-Wunsch alignment:

*** Align3dPlugin ***: 3 arguments:
"1LYZ" PdbDocument 1LYZ
"2LZM" PdbDocument 2LZM
"Protein alignment 6" SequenceAlignmentDocument with 2 sequences:
	"1LYZ" PdbDocument 1LYZ -KVFGRCELAAAMK??RHGLDNYRG...
	"2LZM" PdbDocument 2LZM MNIFEMLRIDEGL??RLKIYKDTEG...
Fixed PDB = 1LYZ, fixed alignment = 1LYZ
Movable PDB = 2LZM, movable alignment = 2LZM
Calling Align3d(1LYZ, 2LZM, alignment of 1LYZ/2LZM)
1LYZ has 129 nodes
2LZM has 164 nodes
Using Dali alignment for 1LYZ
Using Dali alignment for 2LZM
2LZM has 94 links to 1LYZ
2LZM       center at       42.004128       -6.873670       15.785904
1LYZ       center at        2.185106       20.626851       21.652223
Initial error =       17.428050
    1        5.619949
    2        5.504115
    3        5.485816
    4        5.485784
    5        5.485784
    6        5.485784
    7        5.485784
    8        5.485784
    9        5.485784
   10        5.485784
   11        5.485784
   12        5.485784
   13        5.485784
   14        5.485784
   15        5.485784
   16        5.485784
   17        5.485784
   18        5.485784
Rotation matrix:
       0.584392        0.763068       -0.276066 
      -0.441732        0.013763       -0.897042 
      -0.680705        0.646171        0.345114 

New tasks completed:

  1. Now using a single alignment document as the only input. This document may contain more than 2 sequences. The sequences and referenced documents to use are specified in the settings dialog.

  2. Added UI for # iterations, which structure is fixed (reference) and which is movable (aligned):

  3. Added revision data and remarks to aligned file to indicate 3d alignment performed, resulting pre/post translations and rotation matrix, and what 1d alignment was used as input. Two sections in the PDB file (in addition to the coordinates) have been modified. The revision data:

    and the remarks:


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