Difference between revisions of "Protein.m"
(Created page with "Protein data import function. Parses PDB and BMRB data, runs a J-coupling guess, a CSA guess and outputs Spinach data structures. Syntax: [sys,inter]=protein(pd...") |
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| − | Protein data import function. | + | Protein data import function. |
| − | + | ==Syntax== | |
| − | + | [sys,inter]=protein(pdb_file,bmrb_file,options) | |
| − | + | ==Description== | |
| + | This function parses PDB and BMRB data, runs a J-coupling guess using [[guess_j_pro.m]] function, then a backbone CSA guess using [[guess_csa_pro.m]] function, and outputs sys and inter data structures that are required to run by [[create.m]] gateway function in ''Spinach''. | ||
| − | + | ==Arguments== | |
| + | |||
| + | pdb_file - a character string containing the name of the PDB file | ||
| + | |||
| + | bmrb_file - a character string containing the name of the BMRB file | ||
| + | |||
| + | options.select - 'backbone' imports protein backbone up to CB and HB, 'backbone-minimal' only imports | ||
| + | the backbone, 'backbone-hsqc' is the same as backbone, but with GLN and ASN side chain | ||
| + | amide groups included, 'all' imports everything that is assigned in BMRB. If a list of | ||
| + | numbers is supplied, spins with those numbers in the PDB file are imported, but only | ||
| + | if they are assigned in the PDB. | ||
| + | |||
| + | options.pdb_mol - the number of molecule if there are multiple molecules in the pdb file | ||
| + | |||
| + | options.noshift - 'keep' places unassigned atoms between -1 and 0 ppm, 'delete' removes them from the system | ||
| + | |||
| + | ==Returns== | ||
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Note: unassigned atom coordinates are used internally for the J-coupling | Note: unassigned atom coordinates are used internally for the J-coupling | ||
Revision as of 16:46, 8 August 2016
Protein data import function.
Contents
Syntax
[sys,inter]=protein(pdb_file,bmrb_file,options)
Description
This function parses PDB and BMRB data, runs a J-coupling guess using guess_j_pro.m function, then a backbone CSA guess using guess_csa_pro.m function, and outputs sys and inter data structures that are required to run by create.m gateway function in Spinach.
Arguments
pdb_file - a character string containing the name of the PDB file
bmrb_file - a character string containing the name of the BMRB file
options.select - 'backbone' imports protein backbone up to CB and HB, 'backbone-minimal' only imports
the backbone, 'backbone-hsqc' is the same as backbone, but with GLN and ASN side chain
amide groups included, 'all' imports everything that is assigned in BMRB. If a list of
numbers is supplied, spins with those numbers in the PDB file are imported, but only
if they are assigned in the PDB.
options.pdb_mol - the number of molecule if there are multiple molecules in the pdb file
options.noshift - 'keep' places unassigned atoms between -1 and 0 ppm, 'delete' removes them from the system
Returns
Note: unassigned atom coordinates are used internally for the J-coupling prediction procedure, but these atoms are not passed to Spinach.
Note: watch carefully the output of this function, it would inform you if it has to skip an atom or a coupling for any reason.
More information is available in the protein getting started manual.
