Visualization of Multiple Models and Multiple Chains


ProteinShop supports visualization of PDB files containing single and multiple protein structures. There are two types of PDB files containing multiple structures: those that contain Multiple Models and those that contain Multiple Chains. The user can visualize those by editing the ProteinShop's configuration file ("ProteinShop.cfg").

Multiple Models

Usually, NMR results provide different conformations for one structure because the protein sample was in liquid state under NMR experiments. All these conformations are structurally closed to each other. For this kind of PDB file, the user can either show one conformation or superimpose all the conformations. The selection is inside the ProteinCreator section in ProteinShop.cfg file. The default selection is the first model.

For example, to load a single (the first) model from a pdb file :

Section ProteinCreator
...
multipleModel 1
EndSection

Change number 1 to different number(s) for different model(s) selection. To load all the models, either comment out the multipleModel tag or write all the model numbers.

For example, to load the first and third model from a pdb file :

Section ProteinCreator
        ...
        multipleModel 1 3
EndSection

To load all models from a pdb file :

Section ProteinCreator
        ...
 #      multipleModel 
EndSection

Multiple Chains

When a protein structure has more than one chain, ProteinShop may display some or all of its chains. The selection is inside the ProteinCreator section in ProteinShop.cfg file. The default chain selection is "chain A".

For example, to load the chain A from a pdb file :

Section ProteinCreator
...
chainSelection A
EndSection

Change letter A to different letter(s) for different chain(s) selection. To load all the chains, either comment out the chainSelection tag or write all the chain ids.


For example, to load the chain A and C from a pdb file :


Section ProteinCreator
        ...
        chainSelection A C
EndSection


To load all the chains :

Section ProteinCreator
...
# chainSelection
EndSection