PDBRead

Read a PDB file into a MATLAB structure.

Description

PDBRead is a function that will read a Protein Data Bank file into a MATLAB structure.

PDB_struct = PDBRead(filename) reads the file corresponding to filename and stores the information contained in this file in the PDB_struct. e.g. PDB_struct = PDBRead('PDBSilk.txt')

The file that is being read by PDBRead should be compatible to the PDB file format described at the RCSB (Research Collaboratory for Structural Bioinformatics) web site. For more information about this format, please visit the following URL:

http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html

The file "PDBSilk.txt" mentioned in the sample code above was obtained from the following web site:

http://cmm.info.nih.gov/modeling/pdb_at_a_glance.html

The current version of this function can recognize the standard record types mentioned at the above URL. The information stored in the output structure can be extracted by using the . (dot) operator similar to a normal structure in MATLAB. e.g PDB_struct.HEADER will give the information about the HEADER record type.
  
Each record type has format fields. For more information about the fields,please visit the above mentioned URL. Information for each field for a record type can be accessed by using the . (dot) operator. e.g. PDB_struct.HEADER.depDate gives the deposition date for the particular molecule structure. The field names used for a particular record type are according to the information contained at the RCSB web site.

• MATLAB release: MATLAB 6.1 (R12.1)
• Other Files: PDBRead.m, ; PDBSilk.txt

[Ping-Hung Chen]

 

[Joe Cereal]

well, i needed an mfile example of file io with structures.. and this fit the bill nicely.

[Oliver Lange]

Syntax Error when i try to read a pdb-file:
Reference to non-existent field 'REMARK'

[ashiwn rao]

excellent

[Rishi Mukhopadhyay]

Possibly its an issue specific to my setup (Kubuntu linux, matlab 7), but when I run the program on the included PDBSilk.txt file, I get an error message:
??? Cell contents indices must be greater than 0.

Error in ==> PDBRead at 348
                    PDB_struct.SEQRES.ResChainDetail(PDB_struct.SEQRES.NoOfResChain).AminoAcids = strcat(PDB_struct.SEQRES.ResChainDetail(PDB_struct.SEQRES.NoOfResChain).AminoAcids,GetAminoAcids(

[Celso Araujo]

I ger almost the same error as the last poster, under matlab 7.4.0 and linux:

>> p = PDBRead('PDBSilk.txt');
Extracting the information............
??? Subscript indices must either be real positive integers or logicals.
Error in ==> PDBRead at 348
                    PDB_struct.SEQRES.ResChainDetail(PDB_struct.SEQRES.NoOfResChain).AminoAcids = strcat(PDB_struct.SEQRES.ResChainDetail(PDB_struct.SEQRES.NoOfResChain).AminoAcids,GetAminoAcids(