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").
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
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