Chimera X
Open the file with the structure
open PDB ID open 5O1Z (Nrd1, RNA)
open Desktop/Name.pdb(mrc,cxs,etc.)
File -> Open
Movements (using mouse)
Left-click-holding - rotate the structure about the vertical and horizontal axis
Right-click-hold - move the centre of the protein about the screen
Sequence viewer
• Tools -> Sequence -> Show sequence viewer
• Log window -> Click on the link in the Chain informaFon table
• Molecule Display (Analysis sec;on) -> Sequence
Model panel
Structure depic;on
• AcFons - > Atoms/Cartoon/Surface…hide/show
• show atoms/cartoon/surface
hide atoms/cartoon/surface
select
Model ID
color
Select
• Ctrl/(Ctrl+ShiL) + LeLMouse
• Select -> Chains, Chemistry,…
• Sequence viewer
• sel
Nomenclature
#1 => model ID sel #1 (model/structure 1)
/A => chain sel #1/A (model/structure 1, chain A)
:400 => residue number
sel #1/A:464 (one residue nr. 464) - show atoms
sel #1/A:373-414 (residues from 373 to 414)
sel #1/A: 373-414 &:arg (residues from 373 to 414 that are arginines) - show atoms
sel #1/A:378, sel #1/A:342, sel #1/A:376 (residue 378, 342, 376) - show atoms
:arg => all arginines in the selecFon
@ => atom specifier (e.g. @ca). sel #1/A@ca or sel #1/A:400-450@ca
Color
• AcFons -> Color
• color [what] [color] color #1/A red
Zoom
• zoom 1.5
• mouse -> spinning the middle wheel
from N-term to C-term
Hbond
• Tools -> Structure analysis-> H-Bonds
• hbonds hbonds or hbond #1/B or hbond ligand
• hide hbonds
Contacts
• Tools -> Structure analysis-> Contacts
• contacts
contacts #1/A@C* restrict #1/B@C* distance 3.8 reveal true name vdW
Distance/angles
• Tools -> Structure analysis-> Distance
ctrl+shiL and pick the two/three atoms of interest
(Model panel -> distances + distances labels – ediFng)
Surface
• AcFons -> Surfaces-> hide/show
• Tools -> DepicFon -> Surface Color ….by electrostaFcs -> Key. (remove from model
panel)
NMR vs Crystallography
NMR -> bundle of structures (open 2li8)
Tools -> Structure analysis -> Matchmaker
Crystalography -> delete solvent
Hide/delete
• AcFons -> Atoms/Bonds -> Delete
• del del #1/A:400-450
• AcFons -> Atoms/Bonds, Surface,… ->Show/Hide
• hide [what]
Save
File -> Save (cxs, pdb,…)
Tutorials
https://www.cgl.ucsf.edu/chimera/tutorials.html
https://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html