Introduction
Mixed sequence/3D-structure alignments can be computed conveniently by pressing the tool-button JCOMPONENT:StrapView#button(BUT_ALIGN)!.
Please apply the tool-button to the example files BUTTON:Tutorials#bExampleFiles("13")!.
By pressing this button two computational steps are performed automatically.
In this tutorial the two steps are performed manually.
Aligning the PDB-files three-dimensionally
The 3D-coordinates are used to make a multiple sequence
alignment with the superposition program CE or TM-align.
Though the sequences are very different, the WIKI:Protein_structures are similar enough to perform a WIKI:Structural_alignment.
Chose the alignment method COMBO:Superimpose_native_CE or COMBO:Superimpose_CEPROXY in the
dialog BUTTON:DialogAlign!
In this dialog select all proteins with the file suffices ".dssp"
or ".pdb" or ".ent".
Invoke computation with the button LABEL:ChButton#BUTTON_GO.
After successful computation a preview with the resulting alignment is shown.
Press the button LABEL:DialogAlignResult#BUT_LAB_Apply.
Aligning all proteins
Currently, only the proteins with a 3D-structure are aligned.
This alignment will be used as a profile in the following step.
Creating the profile:
Go to BUTTON:DialogExportAlignment! and generate the alignment of the proteins with 3D-structure in
ClustalW format. To avoid that long lines are folded choose a large number for "Residues per line".
Copy the alignment into the text-area for profiles and remove the protein names. Keep only the gapped sequences.
Aligning with the Profile:
Return to the main tab of the dialog BUTTON:DialogAlign!.
Chose the alignment method: WIKI:ClustalW or COMBO:MultipleAlignerT_Coffee and
Select all proteins in the alignment dialog.
Activate the first check-box CB:"profile 1".
When the check-boxes are activated a text-area appears where the profile can be typed in.
Now you can start the computation LABEL:ChButton#BUTTON_GO.
The resulting alignment includes all proteins and respects the previous result of the 3D-alignment.