Bioinformatics Asked by saiden on April 24, 2021
I have a list of PDB IDs with realtive chains that are to be extracted, and the run on dssp
.
For the single chain extraction I tried several methods, such as:
import pymol2
for entry in list:
with pymol2.PyMOL() as pymol:
pymol.cmd.fetch(entry)
pymol.cmd.save(entry + '.cif')
Where, for example, if I want to extract chain AC
for 4YBB
, entry = 4YBBAC
.
This works well in saving the cif files (pymol correctly visualizes them), but makes them not suitable for mkdssp. Indeed, if i run
mkdssp 4YBBAC
I get
DSSP could not be created due to an error:
Is this an mmCIF file?
I tried also using Biopthon:
from Bio.PDB import MMCIFParser
from Bio.PDB.mmcifio import MMCIFIO
parser = MMCIFParser()
io = MMCIFIO()
structure = parser.get_structure("4YBB", "4YBB.cif")
model = structure[0]
chain = model['AC']
io.set_structure(chain)
io.save("4YBBAC.cif")
But again, when running mkdssp, I get:
DSSP could not be created due to an error:
bad lexical cast: source type value could not be interpreted as target
On a closer inspection, both methods drop the columns _atom_site.pdbx_formal_charge _atom_site.auth_comp_id _atom_site.auth_atom_id
from the file, while retaining all the others.
This is the first line of the coordinates from the biopython/pymol file:
ATOM 1 N N . GLY A ? 1 ? -125.713 46.378 -19.108 1.0 77.15 2 AC 1
While this is the original file:
ATOM 34684 N N . GLY C 3 1 ? -125.713 46.378 -19.108 1.00 77.15 ? 2 GLY AC N 1
Is this a bug? Am I using the tools incorrectly? Can my purpose be achieved with other (possibly hassle free) methods?
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