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Python + PyMOL

Python + PyMOL. Arbitrary Python code possible within python scripts PyMOL functionality available by importing PyMOL's modules cmd, cgo, stored etc. Call pymol interpreter, which acts on PyMOL specific code and propagates the rest to

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Python + PyMOL

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  1. Python + PyMOL • Arbitrary Python code possible within python scripts • PyMOL functionality available by importing PyMOL's modules cmd, cgo, stored etc. • Call pymol interpreter, which acts on PyMOL specific code and propagates the rest to • Similar concept in MODELLER (modeling), Chimera, Yasara, VMD (visualization) - they all have Python bindings

  2. Example: Scripted alignment

  3. PyMOL: Center of Mass Calculation Command line execution without graphic interface With graphic interface:

  4. Conservation coloring using Consurf-HSSP • Base: Extracted sequences from SwissProt with high similarity to a certain PDB Entry (HSSP) • Sequence Alignment • Goal: Reflect residue variability in each column on the structural template • Consurf-HSSP: database derivative using Maximum-Likelihood calculation to express residue entropy (round to 1-9)

  5. Consurf-HSSP: Flatfile Data collection • POS: The position of the AA in the SEQRES derived sequence. • SEQ: The SEQRES derived sequence in one letter code. • SCORE: The normalized conservation scores. • 3LATOM: The ATOM derived sequence in three letter code, including the AA's positions as they appear in the PDB file and the chain identifier. • COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable). • MSA DATA: The number of aligned sequences having an amino acid (non-gapped) from the overall number of sequences at each position. • RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.

  6. ConSurf-HSSP Parser – Part I

  7. ConSurf-HSSP Parser – Part II

  8. ConSurf-HSSP Parser – Part III

  9. Conservation: Result in PyMOL

  10. Movie Making • Different Representations • Arbitrary actions using cmd.mdo • Nice effect: Close-up flights over particularly interesting regions Movie control bar

  11. Movie Making: Example Part I

  12. Movie Making: Example Part II

  13. Movie Making: Example Part III

  14. Movie Making: Example Part IV

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