Download www.biotec.tu

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
Example: Scripted alignment
PyMOL: Center of Mass Calculation
Command line execution without graphic interface
With graphic interface:
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)
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 the
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

ConSurf-HSSP Parser – Part I
ConSurf-HSSP Parser – Part II
ConSurf-HSSP Parser – Part III
Conservation: Result in PyMOL
Movie Making


Different
Representations
Arbitrary actions
using cmd.mdo
Nice effect: Close-up
flights over
particularly interesting
regions
Movie control
bar

Movie Making: Example Part I
Movie Making: Example Part II
Movie Making: Example Part III
Movie Making: Example Part IV