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Multi sequence aligment file

  1. Upload FASTA file
    2. Access CLUSTALW, and upload or enter FASTA file. I uploaded five T1 type RNase T1/Po1/He1/Ms/F1, and color-code T1 (PDB ID:2B4U).
    Example of FASTA file

  2. Click "Execute Multiple Aligment"

  3. Save "clustalw.aln"
    4. Example of aligment file


The ConSurf Server

AccessThe ConSurf Server
  1. Analyze Nucleotides or Amino Acids?
    2. →Amino-Acids

  2. Is there a known protein structure?
    3. →YRS
    →Enter PDB ID or upload PDB file

    Click "next"


  3. Do you have a Multiple Sequence Aligment(MSA) to upload?
    4. →Upload aligment file(***.aln)
    →Enter sequence name corresponding PDB file at "Indicate the Query Sequence Name" (PDB ID:2BU4 is corresonds to sequence name T1. So I type T1.)

  4. Do you have a tree file to upload?
    5. →No

  5. Enter Job title and your E-Mail adress, and click "submit"


  6. When the calculation is finished, click "Follow the instructions to produce a PyMol figure (For users of PyMol)"


  7. Save "PDB FILE" and "consurf new.py"



Color-code on PyMOL

  1. Open PDB file
  2. Run → consurf_new.py
  3. Show → surface


    4. Flexible ←--------------------------------------→ Conserved