Haynes:Jmol Guide: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 9: | Line 9: | ||
===Select: Proteins=== | ===Select: Proteins=== | ||
* '''select: all''' - Selects the entire structure. | * '''select: all''' - Selects the entire structure. | ||
* '''select :chainLetter''' - Substitute | * '''select :chainLetter''' - Substitute a letter (a, b, c, etc.) for "chainLetter". This selects a single contiguous peptide in multi-part protein complexes. You can figure out chain letters quickly by trial and error. | ||
* '''select | * '''select residueNumber:chainLetter''' - Substitute "residueNumber" with the number of the amino acid in the protein chain, and "chainLetter" with a, b, c, etc. | ||
==Useful Command Combinations== | ==Useful Command Combinations== | ||
Revision as of 16:58, 18 February 2012
The solved 3D structures for thousands of proteins (many of which are used in our work) are available at the Protein Data Bank (PDB). These are useful for investigating protein structure and function, and for discovering/ designing new modular (BioBrick) parts.
Different regions of the protein, its ligands, subunits, and physical properties can be displayed in different colors, renderings, etc. to make informative images for your web pages, presentations, and posters. Please share helpful tips for using Jmol to accomplish this...
Select: Atoms
Select: Ligands
Select: Proteins
- select: all - Selects the entire structure.
- select :chainLetter - Substitute a letter (a, b, c, etc.) for "chainLetter". This selects a single contiguous peptide in multi-part protein complexes. You can figure out chain letters quickly by trial and error.
- select residueNumber:chainLetter - Substitute "residueNumber" with the number of the amino acid in the protein chain, and "chainLetter" with a, b, c, etc.
Useful Command Combinations
Change the color of a subunit/ chain
Command Lines:
- select :chainLetter; color someColor
Substitute A, B, C, etc. for "ChainLetter". This selects a single contiguous peptide in multi-part protein complexes. Substitute red, blue, yellow, orange, etc. for "someColor."
