pdb(self,
run=None,
file=None,
dir=None,
model=None,
heteronuc='N',
proton='H',
load_seq=1)
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The pdb loading function.
Keyword Arguments
~~~~~~~~~~~~~~~~~
run: The run to assign the structure to.
file: The name of the PDB file.
dir: The directory where the file is located.
model: The PDB model number.
heteronuc: The name of the heteronucleus as specified in the PDB file.
proton: The name of the proton as specified in the PDB file.
load_seq: A flag specifying whether the sequence should be loaded from the PDB file.
Description
~~~~~~~~~~~
To load a specific model from the PDB file, set the model flag to an integer i. The
structure beginning with the line 'MODEL i' in the PDB file will be loaded. Otherwise all
structures will be loaded starting from the model number 1.
To load the sequence from the PDB file, set the 'load_seq' flag to 1. If the sequence has
previously been loaded, then this flag will be ignored.
Once the PDB structures are loaded, unit XH bond vectors will be calculated. The vectors
are calculated using the atomic coordinates of the atoms specified by the arguments
heteronuc and proton. If more than one model structure is loaded, the unit XH vectors for
each model will be calculated and the final unit XH vector will be taken as the average.
Example
~~~~~~~
To load all structures from the PDB file 'test.pdb' in the directory '~/pdb' for use in the
model-free analysis run 'm8' where the heteronucleus in the PDB file is 'N' and the proton
is 'H', type:
relax> pdb('m8', 'test.pdb', '~/pdb', 1, 'N', 'H')
relax> pdb(run='m8', file='test.pdb', dir='pdb', model=1, heteronuc='N', proton='H')
To load the 10th model from the file 'test.pdb', use:
relax> pdb('m1', 'test.pdb', model=10)
relax> pdb(run='m1', file='test.pdb', model=10)
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