PDB files contain information about protein structure. This software bisects the protein into subunits in order to analyze the properties of its fragments. The following type of subunits are defined:
- Amino acid - includes all the atoms of a given residue
- Ramachandran subunit –for amino acid #i includes the atoms: C(i-1)-N(i)-CA(i)-C(i)-N(i+1)
- User defined subunit - with an external atoms.txt file (see format below)
- Amino acid backbone – includes the atoms N-CA-C-O
- Ramachandran with side chain - for amino acid #i includes the atoms: C(i-1)-N(i)-CA(i)-C(i)-N(i+1), the backbone atoms and all the atoms of the side chain
- Ramachandran with side chain and without the backbone oxygen – similar to subunit 5, without the backbone oxygen
Please see below how to create new types of subunits.
- Y. Baruch-Shpigler, H. Wang, I. Tuvi-Arad and D. Avnir, Chiral Ramachandran plots I: Glycine, Biochemistry, 56, 5635-5643 (2017).
- H. Wang, D. Avnir and I. Tuvi-Arad, Chiral Ramachandran Plots II: General trends and proteins chirality spectra, Biochemistry (in press, DOI: 10.1021/acs.biochem.8b00974). 57(45), 6395–6403 (2018).
pdbslicer -
Cut a protein pdb file into subunits.
Version: 0.9.5.3
Usage:
pdbslicer [-o OUTPUT_FILE] [-v ][ -R RANGE ] [-O output_dir] [-M RESNAME] [-C CUTTING METHOD] [-P FILTER] [-A RANGE]
pdbslicer -h
Parameters:
-h Get this help
-i Input pdb file [default is input.pdb]
-O Output directory name
-C Cutting method:
1=cut by amino acid,
2=cut by Ramachandran backbone
3=cut with external "atoms.txt" file. Requires the -a option.
4=cut by amino acid backbone N|CA|C|O atoms
5=cut by Ramachandran with side chain
6=cut by Ramachandran with side chain no oxygen
-a Cut specific atoms of each amino acid. An atoms.txt file should be specified.
-R Model range (1-10,12,14)
-M r Filter by residue name (example: -M GLY)
-P Filter PreProline and Other. Valid values for this parmaeter:
"GENERAL", "PRE_PRO", "GLY", "PRO" or any combination such as "GENERAL|PRE_PRO"
-A a-b Filter by residue sequance number (example: -A 2-8)
-J Do not add time signature to the output directory
-G a-b Create a new PDB file with amino acids a-b. The new file name: old.a-b.pdb
-L Number of subunits in the output files default is 100
-v Verbose output
Eech line of the atoms.txt represnts one amino acid. The file must have 20 lines - one for each amino acid. The line structure is "residue name" then ':' and the chosen atoms seperated by comma. If no atoms are chosen then after the ':' will come the string 'NONE' Here is an example of such a file:
Ala: N,CA,C,O,CB
Arg: ALL ATOMS
Asn: N,CA,C,O,CB
Asp: N,CA,C,O,CB
Cys: N,CA,C,O,CB
Glu: N,CA,C,O,CB
Gln: N,CA,C,O,CB
Gly: N,CA,C,O
His: N,CA,C,O,CB
Ile: N,CA,C,O,CB
Leu: N,CA,C,O,CB
Lys: N,CA,C,O,CB
Met: N,CA,C,O,CB
Phe: N,CA,C,O,CB
Pro: N,CA,C,O,CB
Ser: N,CA,C,O,CB
Thr: N,CA,C,O,CB
Trp: N,CA,C,O,CB
Tyr: N,CA,C,O,CB
Val: N,CA,C,O,CB
The output is in the directory "out_{PDB_NAME}{timestring}" This directory contains:
* cmd_string.txt - the command as typed by the user
* output files - files names are indexed by serial-number + model + peptide-name
This software does not support "alternate location". Please use our "pdb_prep" program.
Data Structures:
pdb object contain one or more models - each model represents protein...
protein is a list of peptides
peptide is a list of atoms
atom has properties such as: X, Y, Z, name, resname, resseq ...