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pdbfixer
PDBFixer fixes problems in PDB files
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Can add hydrogens to nonstandard residues
#295
peastman
opened
1 day ago
0
Bugfixed chain ID assignment in addSolvent (#287)
#294
murfalo
closed
1 week ago
5
Should PDBFixer write out SEQRES entries if provided in the input?
#293
sukritsingh
opened
1 month ago
9
[bug] Ensure numpy < 2 version
#292
awlange
closed
1 month ago
3
PDBFixer adding repeated residues at the start.
#291
Ian-CP
closed
2 months ago
1
Fixing out a very long chain with pdbfixer
#290
stan1233
closed
2 months ago
2
openmm.OpenMMException: Particle coordinate is nan
#289
VeScarecrow
opened
2 months ago
3
How can I cite this tool if I use it
#288
tang2552
opened
2 months ago
1
Error when having more than 10 chain identifiers
#287
FAOlivieri
closed
1 week ago
7
Mutating to non-standard amino acids not present in available force field libraries
#286
amin-sagar
opened
4 months ago
5
mmCIF output - `_atom_site.label_entity_id` not written
#285
Augustin-Zidek
closed
5 months ago
1
fix add missing unknown (UNK) residues error
#284
ndonyapour
opened
6 months ago
3
The repair of two ends of peptide didn't return the desired result
#283
bdx114514
opened
7 months ago
0
How to avoid conflicts with other atoms of the protein when undergoing amino acid mutations?
#282
9527567
closed
7 months ago
2
PDBFixer cannot handle nucleic acids with residue name N
#281
jamesmkrieger
opened
7 months ago
5
Do we have method to mutate the iCode-containing residue?
#280
Loci-Tran
opened
9 months ago
2
findMissingAtoms raises AttributeError if findMissingResidues has not been called first
#279
nielskm
opened
9 months ago
1
pH protonation valid
#278
groponp
opened
9 months ago
1
Issue with Multiprocessing
#277
cplateVT
closed
11 months ago
10
Processed Receptor has Long Legs in PDB File
#276
syedzayyan
closed
11 months ago
14
PDBFixer API cannot fix mmCIF file
#275
Loci-Tran
closed
11 months 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
opened
1 year ago
24
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
`fixer.findMissingResidues()` fails on 3ODU
#255
JSLJ23
closed
1 year ago
2
pypi version
#254
Pantelispanka
opened
1 year ago
9
Select residue atom positions for residues with alternate locations (altloc)
#253
JSLJ23
closed
1 year ago
4
Cannot add missing atoms
#252
kntkb
closed
1 year ago
2
Adding two terminal caps to a single residue
#251
ljmartin
closed
2 years ago
2
Which parameter set(periodicity, offset, k) does PeriodicTorsionForce use in soft.xml?
#250
psp3dcg
closed
1 year ago
8
Version 1.8.1 fails to addSolvent() when boxShape kwarg is present. Also in openmm-setup
#249
pguillem
closed
2 years ago
2
remove
#248
jaredsagendorf
closed
2 years ago
0
Enhancement requests if not already existing?
#247
BJWiley233
opened
2 years ago
5
fix CI badge; remove some old simtk
#246
dwhswenson
closed
2 years ago
1
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