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pdbfixer
PDBFixer fixes problems in PDB files
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fixer.findMissingResidues() could not find the missing residues !
#305
Jalil-Mahdizadeh
opened
14 hours ago
2
Weird coordinates and unable to add Hydrogens upon adding tyrosines
#304
sukritsingh
opened
3 days ago
5
Added optimizeHydrogenBonds()
#303
peastman
opened
2 weeks ago
0
app.Modeller._loadStandardHydrogenDefinitions() AttributeError: type object 'Modeller' has no attribute '_loadStandardHydrogenDefinitions'
#302
MichaelAbel1
closed
3 weeks ago
2
Neutralise systems with formal charges from the PDB
#301
Yoshanuikabundi
opened
3 weeks ago
4
findMissingResidues does not detect residues missing from structure
#300
YoavShamir5
closed
4 weeks ago
10
`PDBFixer.addSolvent` often incorrectly neutralises systems with charged ligands as though they were neutral
#299
Yoshanuikabundi
opened
1 month ago
7
Fixed bug in added bonds to heterogens
#298
peastman
closed
1 month ago
1
PDBFixer not writing out complete CONECT records for downloaded Templates
#297
sukritsingh
closed
1 month ago
10
Support nonstandard residues
#296
peastman
closed
1 month ago
0
Can add hydrogens to nonstandard residues
#295
peastman
closed
1 month ago
1
Bugfixed chain ID assignment in addSolvent (#287)
#294
murfalo
closed
1 month ago
5
Should PDBFixer write out SEQRES entries if provided in the input?
#293
sukritsingh
opened
2 months ago
9
[bug] Ensure numpy < 2 version
#292
awlange
closed
2 months ago
3
PDBFixer adding repeated residues at the start.
#291
Ian-CP
closed
3 months ago
1
Fixing out a very long chain with pdbfixer
#290
stan1233
closed
4 months ago
2
openmm.OpenMMException: Particle coordinate is nan
#289
VeScarecrow
opened
4 months ago
3
How can I cite this tool if I use it
#288
tang2552
opened
4 months ago
1
Error when having more than 10 chain identifiers
#287
FAOlivieri
closed
1 month ago
7
Mutating to non-standard amino acids not present in available force field libraries
#286
amin-sagar
opened
5 months ago
5
mmCIF output - `_atom_site.label_entity_id` not written
#285
Augustin-Zidek
closed
7 months ago
1
fix add missing unknown (UNK) residues error
#284
ndonyapour
opened
8 months ago
3
The repair of two ends of peptide didn't return the desired result
#283
bdx114514
opened
8 months ago
0
How to avoid conflicts with other atoms of the protein when undergoing amino acid mutations?
#282
9527567
closed
8 months ago
2
PDBFixer cannot handle nucleic acids with residue name N
#281
jamesmkrieger
opened
9 months ago
5
Do we have method to mutate the iCode-containing residue?
#280
Loci-Tran
opened
10 months ago
2
findMissingAtoms raises AttributeError if findMissingResidues has not been called first
#279
nielskm
opened
10 months ago
1
pH protonation valid
#278
groponp
opened
11 months ago
1
Issue with Multiprocessing
#277
cplateVT
closed
1 year ago
10
Processed Receptor has Long Legs in PDB File
#276
syedzayyan
closed
1 year ago
14
PDBFixer API cannot fix mmCIF file
#275
Loci-Tran
closed
1 year ago
5
Invalide chirality when fixing neural network generated structure
#274
ryankzhu
opened
1 year ago
3
Updated version number to 1.9
#273
peastman
closed
1 year ago
0
PDBfixer with python=3.10 and openmm=7.7
#272
matteo-cagiada
closed
1 year ago
2
pdbfixer doesn
#271
matteo-cagiada
closed
1 year ago
0
Is there any molecular dynamics or docking research published using pdbfixer?
#270
RuikangSun
opened
1 year ago
5
[Unexpected behaviour] Unexpected behavoiur when parsing mmCIF files
#269
Croydon-Brixton
opened
1 year ago
5
Optimizations to _findNearestDistance()
#268
peastman
closed
1 year ago
2
Speed up _findNearestDistance
#267
edwag
closed
1 year ago
4
Missing b factors
#266
zlcrrrr
closed
1 year ago
2
Updated installation instructions
#265
peastman
closed
1 year ago
0
For those care about the running time
#264
Minys233
closed
1 year ago
3
Allow initialization from topology, positions, and sequence.
#263
jonathanking
opened
1 year ago
1
Add forcefield argument to addMissingHydrogens.
#262
jonathanking
closed
1 year ago
1
Add phosphorylated residues SEP and PTR (pSer and pTyr)
#261
sukritsingh
closed
1 month ago
25
Residues are not recorded correctly
#260
Ruibin-Liu
opened
1 year ago
1
Adding phosphorylated residues to PDBFixer templates
#259
sukritsingh
opened
1 year ago
12
Add nonstandard residue '5OW' to LYS
#258
Ruibin-Liu
closed
1 year ago
10
Added nonstandard residue 'MK8'
#257
Ruibin-Liu
closed
1 year ago
0
Failed to find missing residues in 6VYC
#256
jw-feng
closed
1 year ago
6
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