Protein-RNA interactions of1 3 1.04.2016
Vizualization of structures by PyMol
Disclaimer: any structure is just a model!
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Get the pdb: pdb.org or pdbe.org
Documentation about pdb file format: http://www.wwpdb.org/documentation/file-format
Example:
- go to pdb.org -> type in search ‘Nrd1’-> download entries 2LO6 and 3CLJ
- open with text reader
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Download Pymol: http://www.pymol.org/
Manuals and hints: http://pymolwiki.org or type help
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To load pdb-file:
• open Pymol -> File -> Open
or
• type fetch PDBID
Save pymol session:
• Pymol -> File -> Save session as …
or
• save folder/folder/…/thisSession.pse
To save logs for the session and use later as a script:
• File -> Log or log_open log1.pml
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To see sequence:
• button S in the right bottom corner
or
• type set seq_view, 1
Pymol panels:
A - action
S - show
H - hide
L - label
C - color
Protein-RNA interactions of2 3 1.04.2016
Vizualization modes:
lines (e.g. show lines)
sticks
cartoon (use dss, dss defines secondary structure based on backbone geometry
and hydrogen bonding patterns)
ribbon
surfase
spheres
Color:
by element
by secondary structure
by chain
Selection: http://pymol.sourceforge.net/newman/user/S0220commands.html
select name, (selection)
atom type: name or n.,
select carbons, name ca+cb+cg+cd
residue type: resn or r.,
select aas, resn asp+glu+asn+gln ; select bases, resn a+g
residue number: resi or i.,
select nterm, resi 1-10
chain: chain or c.,
select firstch, chain a
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NMR structures (try on 2LO6):
• to see the whole bundle set all_states, on
• to align states intra_fit PDBID
• to split all states as separate objects split_states PDBID
• hide hydrogens hide (hydro)/show (hydro)
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X-ray structures (try on 3CLJ, 2GQW)
Lamb, A.L., Kappock, T.J., and Silvaggi, N.R. (2015). You are lost without a map: Navigating the sea of
protein structures. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1854, 258–268.
• color by chain
• split chains: split_chains
• hide water hide (solvent)
• add hydrogens: action -> hydrogen -> add
• select water select water, resn hoh
• color by B-factor:
spectrum b, blue_white_red, minimum=20, maximum=50
as cartoon
cartoon putty
• generation of symmetry and electron density maps (http://
pymol.sourceforge.net/newman/user/S0400xtal.html)
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Protein-RNA interactions of3 3 1.04.2016
Electrostatics (to see positive, negative, neutral areas)
Action -> generate -> vacuum electrostatics -> protein contact potential
Distance measurements
Wizard -> measurement
distance test, 10/CA, 50/CA
select around10, i. 12 a. 10
Hydrogen-bonds: http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/
Katsutani/en/hydrogenbond.php
Action -> find-> polar contacts -> select from menu
Get surface : http://www.pymolwiki.org/index.php/Get_Area
1. select area of interest -> Action -> duplicate
2. Action -> compute -> select from menu
Alignment
1. Load structures of interest
2. Action -> align -> to molecule
several alternatives: http://pymolwiki.org/index.php/
Cealign#Multiple_Structure_Alignments
Interface residues: http://www.pymolwiki.org/index.php/InterfaceResidues
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Vizualization for publication: http://www.pymolwiki.org/index.php/
Publication_Quality_Images
bg_color white
ray 1000, 1000
save test_image.png
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Scripting: http://pymolwiki.org/index.php/Simple_Scripting
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Multiple sequence alignment visualisation: ConSurf server http://consurf.tau.ac.il/
LigPlot: Automatically generates schematic diagrams of protein-ligand interactions for a
given PDB file. http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/
UCSF Chimera - more sophisticated then PyMol : https://www.cgl.ucsf.edu/chimera/