Select a file (.pdb)
   Chains to visualize (ex: A,D):
or enter a PDB Id   (ex: 1tim, 1timA)
(optional) Trajectory (.xtc,.dcd,.crd)

Here is a tool to visualize the sequence of a PDB file (and get the correct residue numbers).

Default representation :

Title :
Sub-Title file (?):    
Advanced parameters
Display:
Backbone :
as :
Color :
view named colors
SideChains :
as :
Color :
Heteros :
as :
Color :
Surface :
Opacity :
Color :
Advanced parameters
Scene (?):
Centre on :   (ex: A.CYS3.CA)
Focus on :   (ex: A.CYS3.SG)
View Angle :
Picture:
Background (?):
Image Size :
Format :
Produce :
Animation:
Scenarii (?):
Renderer :
Camera (?):
Advanced parameters
 
Frames :
Step :
Delay :
 
Orientation panel (?): This panel defines animation scenario by assigning objects (chains or ligands) to cells that mimick the display (split in a 3x3 matrix). Click here for more details or have a look at the animation Quick-Start.
Chains Pr:
Xrot
Yrot
Zrot
Chains Pr:
Xrot
Yrot
Zrot
Chains Pr:
Xrot
Yrot
Zrot
Chains Pr:
Xrot
Yrot
Zrot
Chains Pr:
Xrot
Yrot
Zrot
Chains Pr:
Xrot
Yrot
Zrot
Chains Pr:
Xrot
Yrot
Zrot
Chains Pr:
Xrot
Yrot
Zrot
Chains Pr:
Xrot
Yrot
Zrot
 Rot. order:

N.B. for the preview : Jre 1.5 or higher required. In case of problem please read this note (page bottom). Windows XP users, please consider using Firefox or Opera for this previewer to work correctly. We have noticed strange behaviour on applet download using Internet Explorer.

 

Supplementary representations:
You can specify specific representations for selections. see the Help page

Selection1 :
   Display as :
   Color :    view named colors
Selection2 :
   Display as :
   Color :    view named colors
Selection3 :
   Display as :
   Color :    view named colors
Selection4 :
   Display as :
   Color :    view named colors
Selection5 :
   Display as :
   Color :    view named colors
Selection6 :
   Display as :
   Color :    view named colors
Selection7 :
   Display as :
   Color :    view named colors
Selection8 :
   Display as :
   Color :    view named colors

 

Advanced parameters:

Title options:     back to basic parameters
Position (pixels) X :
     Y :
Font :
Size :
Face :
Color : view colors
Sub-Title options:     back to basic parameters
Position (pixels) X :
     Y :
Font :
Size :
Face :
Color : view colors
Focus options:     back to basic parameters
   X trn :
   Y trn :
   Z trn :

Color options:     back to basic parameters   view colors
helix :
strand :
coil :
positive :
negative :
neutral :
 
carbon :
nitrogen :
oxygen :
sulfur :
phosphor :
hydrogen :
iron :
 
ALA :
ARG :
ASN :
ASP :
CYS :
GLN :
GLU :
GLY :
HIS :
ILE :
LEU :
LYS :
MET :
PHE :
PRO :
SER :
THR :
TRP :
TYR :
VAL :
 
backbone :
side-chains :
TFac1From Color:
TFac1ToColor :
TFac1From :
TFac1To :
TFac2From Color :
TFac2To Color :
TFac2From :
TFac2To :
 
1st chain :
2nd chain :
3rd chain :
4th chain :
 
hydrophobic :
hydrophylic :
basic :
acidic :
polar :
aromatic :
aliphatic :
Rendering options (?) :     back to basic parameters
   Radiosity :
   Material reflection :
   Light :
   Depth cueing :