Chimera X

Open the file with the structure

open PDB ID     open 5O1Z  (Nrd1, RNA)

open Desktop/Name.pdb(mrc,cxs,etc.)

File -> Open

A screenshot of a computer Description automatically generated

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 information table

·         Molecule Display (Analysis section) -> Sequence  A screenshot of a computer Description
automatically generated

Model panel

Textové pole: color Textové pole: Model ID Textové pole: select A screenshot of a computer
Description automatically generated

Structure depiction

·         Actions - > Atoms/Cartoon/Surface…hide/show

·         show
atoms/cartoon/surface
                                                                         hide
atoms/cartoon/surface

Select

·         Ctrl/(Ctrl+Shift) + LeftMouse

·         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 selection

@ => atom specifier (e.g. @ca).  sel #1/A@ca  or sel #1/A:400-450@ca


Color

·         Actions -> Color

·         Textové pole: from N-term to C-term color [what] [color]    color #1/A red

Zoom

·         zoom 1.5

·         mouse -> spinning the middle wheel





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+shift and pick the two/three atoms of interest

(Model panel -> distances + distances labels – editing)

Surface

·         Actions -> Surfaces-> hide/show

·         Tools -> Depiction -> Surface Color ….by electrostatics -> Key.  (remove from model
panel)

NMR vs Crystallography

NMR -> bundle of structures  (open 2li8)

Tools -> Structure analysis -> Matchmaker

Crystalography -> delete solvent

Hide/delete

·         Actions ->  Atoms/Bonds -> Delete

·        del                                  del #1/A:400-450

·         Actions ->  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