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one case cannot fix missing residue #241
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Can you create a simpler example that uses only PDBFixer, without Biopython or PDBTools? It can download the PDB file for you, so you don't need anything else to do that: fixer = PDBFixer(pdbid='6hqv') It also can remove the unwanted chains with |
I evaluate it with only PDBFixer. fixer.removeChains cannot seperate chainA. I guess biopython and PDBtools also have problem for these issue.
download_pdb(pdbid='6hqv') output have below results and
when I check original PDB file 6hqv,
so when I check the sequence, it show two chain.
I rerun load PDB file and select chain A, it eliminate GLU in chain B. |
I implement it with redundant script. it make output what I expected.
|
I evaluate OpenMM simulation and the output works well. |
I evaluate one chain from complex assembly pdb file(6HQV).
when I select chain A with biopython, it detect discountinous but it cannot detect missing residue with PDBFixer.
and it pass on energy minimizing step but cause the
NaN position error
in OpenMM simulation iteration.However, when I select chain A with PDBTools, it detect lots of missing residues with PDB Fixer,
but it also fail on energy minimizing step with error
ValueError: No template found for residue 1590 (GLU). The set of atoms is similar to DC5, but it is missing 10 atoms.
How could I fix this issue?
thanks
below is detail log. custom script is also attached in the bottom.
I guess it would be dashed line in the 3D view in RCSB site
ValueError: Particle position is NaN
. detail log is below :error log NaN postion
it seems that PDBFixer detect missing residues well as expected.
after fix, I could see the added residues as reported.
ValueError: No template found for residue 1590 (GLU). The set of atoms is similar to DC5, but it is missing 10 atoms.
it's odd error becuase, it has 1589 residues and end is not GLU(E) but HIS(H) in the fixed PDB. .
detail error below :
when I check the whole sequence, fixed pdb have two chain. second chain include only residue E.
it seems that cause the error.
it's google drive link for all PDB_files
-------------------- below is utility script what I test --------------------
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