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MOL2 Format
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Settings Only
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Build
Fragment
Methane
Acetylene
Amide N->C
Amide C->N
Carbonyl
Cyclobutyl
Cyclopentyl
Cyclopentadiene
Cyclohexyl
Cycloheptyl
Sulfonyl
Residue
Alanine (ALA)
Arginine (ARG)
Asparagine (ASN)
Aspartate (ASP)
Cysteine (CYS)
Glutamine (GLN)
Glutamate (GLU)
Glycine (GLY)
Histidine (HIS)
Isoleucine (ILE)
Leucine (LEU)
Lysine (LYS)
Methionine (MET)
Phenylalanine (PHE)
Proline (PRO)
Serine (SER)
Threonine (THR)
Tryptophan (TRP)
Tyrosine (TYR)
Valine (VAL)
Acetyl Cap (ACE)
N-Methyl Cap (NME)
Amine Cap (NHH)
Secondary Structure
Helix
Antiparallel Beta
Parallel Beta
Replace Atom
Carbon
Nitrogen
Oxygen
Sulfur
Phosphorus
Fluorine
Chlorine
Bromine
Iodine
Cycle Bond Valence
Fill Hydrogens
Invert
Create Bond
Remove Atom
Charge
+1 Formal Charge
-1 Formal Charge
0 Formal Charge
Sculpting
Auto-Sculpting (toggle)
Sculpting (toggle)
Activate (all)
Deactivate (all)
Cycles per Update
1
10
100
Movie
Append
0.5 second
1 second
2 seconds
4 seconds
8 seconds
15 seconds
30 seconds
60 seconds
Program
Camera Loop
X-Rock
30 deg, 4s
30 deg, 8s
60 deg, 8s
60 deg, 16s
Y-Rock
30 deg, 4s
30 deg, 8s
60 deg, 8s
60 deg, 16s
X-Roll
4 seconds
8 seconds
16 seconds
Y-Roll
4 seconds
8 seconds
16 seconds
Nutate
15 deg, 4s
15 deg, 8s
30 deg, 8s
State Loop
Full Speed
1/2 Speed
1/4 Speed
1/8 Speed
State Sweep
Full Speed
1/2 Speed
1/4 Speed
Play
Stop
Rewind
Reset (clear movie)
Frame Rate
30 FPS
15 FPS
5 FPS
1 FPS
Loop Frames
Show All States
Movie Panel
Cache Frames
Display
Sequence Viewer
Sequence Mode
Residue Codes
Residue Names
Chain Identifiers
Atom Names
Stereo
Off
Anaglyph
Cross-Eye
Wall-Eye
Color Space
CMYK (Print)
ViewMol (Default)
RGB
Grid
By Object
By State
Disable
Background
Black
White
Grey
Light Grey
Quality
Maximum Quality
Reasonable Quality
Reasonable Performance
Maximum Performance
Depth Cue (Fog)
Two-Sided Lighting
Specular Reflections
Orthoscopic View
Show Valences
Animation
Zoom
Zoom All
Zoom Complete
8 A Sphere
12 A Sphere
20 A Sphere
Clipping
Nothing
8 A Slab
16 A Slab
30 A Slab
Show
Lines
Sticks
Cartoon
Spheres
Surface
Mesh
Ribbon
Dots
Nonbonded Spheres
As (replace)
Lines
Sticks
Cartoon
Spheres
Surface
Ribbon
Hide
Lines
Sticks
Cartoon
Spheres
Surface
Mesh
Ribbon
Dots
Everything
Color
By Element
Default (C=green)
C=cyan, rest by element
C=yellow, rest by element
C=white, rest by element
C=magenta, rest by element
Spectrum
Rainbow
B-factor
By Chain
By Sec. Structure
Cyan
Green
Yellow
Orange
Salmon
Red
Magenta
Purple
Blue
Marine
White
Grey
Setting
Transparency
Surface: 0%
Surface: 20%
Surface: 40%
Surface: 60%
Surface: 80%
Cartoon: 0%
Cartoon: 40%
Cartoon: 60%
Stick: 0%
Stick: 40%
Stick: 60%
Cartoon
Auto (Fancy Helices)
Tube
Putty (B-factor)
Side Chain Helper
Round Helices
Sticks
Ball and Stick
Radius 0.1
Radius 0.2
Radius 0.25 (default)
Label
Label Residues
Label Chains
Label Atoms
Clear Labels
Size: 14pt
Size: 24pt
Size: 36pt
Surface
Solid
Wireframe
Dots
Solvent Accessible
Cavity Mode
Off
Cavities Only
Cavities + Pockets
Rendering
Shaders (toggle)
Shadows (toggle)
Antialias
Off
FXAA
SMAA
Lines
Width 1.0
Width 1.5
Width 3.0
Lines As Cylinders
Label Font
Sans (Default)
Serif
Mono
Sans Bold
Serif Bold
Auto-Show
Lines
Spheres
Cartoon
Sticks
Nonbonded Spheres
Mouse
Selection Mode
Atoms
Residues
Chains
Segments
Objects
Molecules
C-alphas
3 Button Viewing
3 Button Editing
2 Button Viewing
1 Button Viewing
Virtual Trackball
Preset
Simple (cartoon + lines)
Technical
Publication Quality
Pretty
Ball and Stick
Default (lines)
Wizard
Measurement
Mutagenesis
Label
Pair Fitting
Sculpting
Density Map
Filter
View
Reset View
Orient
Center
Rotate
X +90
X -90
Y +90
Y -90
Z +90
Z -90
Scene
Next
PgDn
Previous
PgUp
Append (Store New)
Append Variant
Camera Only
Object Colors Only
Reps Only
Reps + Colors
Update Current
Delete Current
Clear All Scenes
Recall
F1
F2
F3
F4
F5
F6
F7
F8
F9
F10
F11
F12
Store
F1
F2
F3
F4
F5
F6
F7
F8
F9
F10
F11
F12
Scene Buttons
Help
Command Reference
PyMOL Wiki (Upstream)
Selection Algebra
PyMOL Docs (Upstream)
How to Cite PyMOL (Upstream)
About ViewMol
Objects
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Measurement
×
Mode:
Distances
Angles
Dihedrals
Polar Contacts
Neighbors
Object:
Merge
New Object
Delete Last
Delete All
Done
Click first atom...
Mutagenesis
×
Target:
ALA - Alanine
ARG - Arginine
ASN - Asparagine
ASP - Aspartate
CYS - Cysteine
GLN - Glutamine
GLU - Glutamate
GLY - Glycine
HIS - Histidine
ILE - Isoleucine
LEU - Leucine
LYS - Lysine
MET - Methionine
PHE - Phenylalanine
PRO - Proline
SER - Serine
THR - Threonine
TRP - Tryptophan
TYR - Tyrosine
VAL - Valine
<
Rotamer 1/1
>
Apply
Clear
Done
Click a residue to mutate...
Label
×
Format:
Residue Name + Number
One Letter + Number
Atom Name
Element
Chain
Residue Number
Residue Name
B-factor
Occupancy
Clear All Labels
Done
Click atoms to label...
Pair Fitting
×
0 pairs defined
Fit Pairs
Delete Last
Clear
Done
RMSD: --
Pick mobile atom...
Sculpting
×
Radius:
6 A
8 A
10 A
15 A
20 A
Toggle Sculpting
Toggle Bumps
Done
Pick center atom...
Density Map
×
Contour:
1.0
Radius:
5 A
8 A
10 A
15 A
Update Maps
Next Residue
Prev Residue
Done
Load a map to begin...
Filter
×
Browse:
All
Accepted
Rejected
Deferred
State 1/1
Accept
Reject
Defer
Back
Forward
Done
Select multi-state object...
Press / for commands | Drag to rotate | Scroll to zoom
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