The PYMOL Molecular Graphic System

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The PYMOL Molecular Graphic System
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PYMOL

• It supports Windows, Linux, Solaris, Macintosh,
  IRIX
• Freely available _at_ http//delsci.com/rel/099/

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Basic modules
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Load your pdb file
External GUI file-open Command lines load
file-path (e.g., load c/1hng.pdb)
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Load files
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Load data-file-name
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Important panels
Actions Show Hide Color
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Manipulate your objects
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Right click your mouse more options
Right click more choices
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Different visual effects
Stick
Ribbon
Surface
Cartoon
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Different way of cartoon presentation
automatic
tube
putty
loop
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Manipulate the view by mouse
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Measure distances
External GUI wizard-measurement Then click the
target atoms
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Find polar contacts
Name panel your selected residues Actions-Find-Po
lar contacts-
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Make Mutation
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Overlay two structures
Align filenameA//2-240/CA, filenameB//2-240/CA
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Plugin
Need install APBS and PDB2PQR in Linux system
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DIY

• Build your molecule
• Adjust your mutated side-chain to expected
  location
• Polish PDB file

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Make movies
Util.mrock(start,finish,angle,phase,loop-flag) Uti
l.mroll(start,finish,loop-flag) e.g., load
c/3cln.pdb mset 1 x60 util.mrock 1,60,90,1,1
Create a 60 frame movie with /- 90 deg. rock
Create full rotation around the Y axis over 60
frames
load c/3cln.pdb mset 1 x60 util.mrock 1,60,1
XnView and UnFreez
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How to Open files
External GUI file-open Command lines load
file-path
How to save your work
External GUI file-save session or save
image Command lines png file-name
Use ray will give you better visual effects!!!
How to measure distance
External GUI wizard-measurement Then click the
target atoms
How to show polar contact (H-bonding)
Name panel A-find-polar contacts
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How to select residues
Left click the residue Or use select
command Select resi 1012 /select resi 10
and 12/ Select resi 10-20 /select resi
from 10 to 20/
How to show metal ions
Read the pdb file, get the resi (say, 164) of
metal ions
Type in the command line select resi 164 Go to
the name panel corresponding to your selection
Click S- spheres /show the metal as
spheres/ Sometimes, you can use command line
show spheres, het /shows all the atoms defined
as HETATOMS/ Go to the name panel corresponding
to your selection Click H-waters /hide
waters/