Structure Visualization with PyMOL

Transcription

1 BINF 6202/ITSC 8202, Spring 2011 Structure Visualization with PyMOL February 8, 2011

2 Structure Visualization Why: to see the structure at different level of details + to show the structure Software: Jmol, MDL Chime, PyMOL, RasMol, UCSF Chimera, VMD, Why PyMOL: 1. Publication-quality rendering of molecular structures 2. Free (pre-1.0 versions) 3. Easy to use For reference, visit

3 1. Load a structure file. 2. Styles of visualization. 3. Selective visualization. 4. Structure images. Structure Visualization with PyMOL

4 PyMOL User Interface Menus and commands Text output Command line Graphical output Object control panel Objects Mouse commands Command line

5 PyMOL User Interface 3-button mouse control Mouse modes & selection modes Actions Show Hide Label Color

6 PyMOL Command Options 1. Getting a structure: >fetch PDBCODE, File -> Open 2. Selecting what to visualize: >select name, selection Matching Property Selector symbol name resn Identifier and Example chemical symbol list (> select polar, symbol o+n) atom name list (> select carbons, name ca+cb+cg+cd) residue name list (> select aas, resn asp+glu+asn+gln) resi residue identifier list (> select mults10, (resi 1+10 or resi 20 30)) alt alternate conformation identifier list (> select altconf, alt a+ ) chain chain identifier list (> select firstch, chain a) ss secondary structure type (> select allstrs, ss h+s+l+ ) Reference:

7 PyMOL Command Options Operator not s1 s1 and s2 s1 or s2 Effect Selects atoms that are not included in s1 > select sidechains,! bb Selects atoms included in both s1 and s2 L> select far_bb, bb &farfrm_ten Selects atoms included in either s1 or s2 > select all_prot, bb sidechain 3. Styles of visualization: >show representation, (object or selection) >show cartoon, chain a+b >show spheres, name ca (Optional) Polishing the visualization: >ray width, height 4. Saving PyMOL session: File -> Save Session As Visualization: File -> Save Image As -> PNG `

8 Demonstrations 1. Visualizing the whole structure 2. Visualizing part of a structure 3. Visualizing the hydrogen bond network in a protein-dna complex

9 Example 1: Visualizing the Whole Structure The lines starting with > are command line options. The lines starting with # are for menu selections. The lines starting are for the object panel. For >A means clicking the A at the right of the p object name. 1. Load a structure >fetch 1ttu 2. Remove water and hetero molecules >remove resn hoh >remove resn edo 3. Set the background color to white #Display > background > white 4. Make the protein as an object >select p, chain a 5. Make a DNA object >select d, chain b+c 6. Copy the protein to make another protein object for surface >A >copy to >A >rename >p_surf

10 Example 1: Visualizing the Whole Structure 7. Copy the DNA to make another DNA object for surface >A >copy to >A >rename >d_surf 8. Show the cartoon representation of protein and >S >as >S >as >cartoon 9. Color the protein cartoon according to secondary >C >by ss >(choose any ss color scheme) 10. Color DNA cartoon according to >C >by element >(choose any element color scheme) 11. Show protein and DNA >S >as >S >as >surface 12. Color protein and DNA >C >(any >C >(any color) 13. Make protein and DNA surfaces transparent >set transparency=0.6, p_surf >set transparency=0.6, d_surf

11 Example 2: Visualizing Part of a Structure 1. Load a structure >fetch 1ttu 2. Remove water and hetero molecules >remove resn hoh >remove resn edo 3. Set background white #Display > background > white 4. Make a protein object >select p, chain a 5. Make a DNA object and show it as a cartoon >select d, chain >S >as >cartoon 6. Make an object of protein heavy atoms within 10 angstroms from any DNA heavy atom >select pard, p w. 10 of d

12 Example 2: Visualizing Part of a Structure 7. Show only pard instead of the whole protein, in stick >H >S >as >sticks 8. Make a surface object for >A >copy to >A >rename >(type any name such as pard_surf >S >as >C >(choose any color) >set transparency=0.6, pard_surf 9. Make a surface object for >A >copy to >A >rename >(type any name such as d_surf >S >as >C >(choose any color) >set transparency=0.6, d_surf