RosettaCommons / RosettaCommons/PyRosetta.notebooks
ERROR/warning when read pdb files
Open
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 709
- Forks
- 173
- Avg merge
- 5m
- Merged PRs (30d)
- 2
Description
I want to know whether the following ERROR/warning matters when I mutate amino acids in pyrosetta:
core.import_pose.import_pose: File '/data2/rjli/test_dataset/1amk/1amk_protein.pdb' automatically determined to be of type PDB
core.io.pdb.HeaderInformation: [ WARNING ] Deposition day not in range [1, 31]: 0
core.io.pdb.HeaderInformation: [ WARNING ] Unrecognized month in HEADER deposition date
core.io.pdb.HeaderInformation: [ ERROR ] Malformed Compound record found: ' 1AMK_PROTEIN'
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] discarding 4 atoms at position 1 in file /data2/rjli/test_dataset/1amk/1amk_protein.pdb. Best match rsd_type: SER:NtermProteinFull
THE PYTHON CODE :
import os
from pyrosetta import *
from pyrosetta.rosetta.protocols.simple_moves import MutateResidue
init()
source_folder = '/data2/rjli/test_dataset'
for id in os.listdir(source_folder):
folder_path = os.path.join(source_folder, id)
if os.path.isdir(folder_path):
for file in os.listdir(folder_path):
if file.endswith('protein.pdb'):
protein_file = os.path.join(folder_path, file)
pose = pose_from_pdb(protein_file)
n_res = pose.total_residue()
# loop over all residues
for i in range(1, n_res + 1):
res = pose.residue(i)
if res.name() == "ASN":
# create a MutateResidue mover to mutate Asn to Leu
mut = MutateResidue(i, "LEU")
mut.apply(pose)
if res.name() == "GLN":
# create a MutateResidue mover to mutate GLN to Leu
mut = MutateResidue(i, "LEU")
mut.apply(pose)
output_file = os.path.join(folder_path, f'{id}_mutate0_protein.pdb')
pose.dump_pdb(output_file)
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the supplied Python loop and its pose_from_pdb call, then inspect the input PDB header and compound records alongside the reported discarded atoms. Determine whether the warnings change the loaded pose or the subsequent mutations; the issue is done when the impact of each message and any required input correction are documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100