To extract a FASTA sequence from a PDB deposit:
seqc -in:pdb=19hc_A1.pdb -out::fasta
To cut a substructure of a PDB deposit:
strc -in::pdb=2gb1.pdb -select::substructure=A:1-15 -out::pdb=fist15.pdb
The command will cut residues from 1 do 15 from chain A and print them in PDB format to
fist15.pdb file. To print the output on the screen, say just
-out::pdb (without any file name)
Calculate backbone dihedral angles (Ramachandran map)
str_calc -in::pdb=2azaA.pdb -calc::phi_psi
Calculate a map of minimal distances between residues in a given structure
str_calc -in::pdb=2azaA.pdb -calc::distmap::min -calc::distmap::describe
For every pair of residues the minimal distance between their atoms is reported.
option turns on detailed numbering of residues in the output, making it much bigger.
See also this tutorial about distance maps produced by BioShell
Calculate structure alignment between two protein chains: 2azaA and 2pcyA:
str_align -in::pdb=2azaA.pdb -in::pdb::native=2pcyA.pdb -d=/home/user/bioshell/data
Result that will be printed on the screen provides information on tm-score values, crmsd distance, coverage as well as the alignment itself. For a shorter (tabular) form of the ouput, add option
-str_align::out::tabular, as in the following example:
Calculate multiple structure alignments and get results as a flat table.
str_align -in::pdb::listfile=2gb1-models.txt -in::pdb::native=2gb1A.pdb -str_align::out::tabular
This command will read a file
2gb1-models.txtthat lists PDB files and calculate a structure alignment for each of these models with the native structure.