salilab pmi issues - Githubissues

salilab / pmi

Python Modeling Interface

https://integrativemodeling.org/nightly/doc/ref/namespaceIMP_1_1pmi.html

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issues

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Close NestOR rmf file

#264 shreyas-arvindekar closed 8 months ago
1
Additions to EM and crosslinking restraints. Minor modifications in ReplicaExchange macro

#263 shreyas-arvindekar closed 8 months ago
3
Different behavior between different runs when adding SAXS restraint

#262 ajtritt closed 1 year ago
2
Unable to read PDB 7KOE

#261 ajtritt closed 1 year ago
1
Remove use of get_is_canonical()

#260 benmwebb closed 1 year ago
0
ValueError: The system contains at least one chain ID (AA) that is more than 1 character long

#259 almara3 closed 2 years ago
2
Lock access to best.scores.rex.py file

#258 benmwebb closed 2 years ago
1
Allow creating more than 62 proteins with TopologyReader

#257 benmwebb closed 3 years ago
0
Warn when creating a molecule with name ending in .(some number)

#256 benmwebb closed 3 years ago
0
Fixes pmi single rigid body shuffle issue

#255 Stochastic13 closed 3 years ago
1
PMI shuffle_configuration does not work with a single rigid body

#254 Stochastic13 closed 3 years ago
1
Fixes pmi shuffle issue

#253 Stochastic13 closed 3 years ago
1
Attempting to retain the same chain ids in the model as in pdb files supplied with a topology file, causes a seg-fault.

#252 tanmoy7989 closed 3 years ago
2
TopologyReader fails if PDBs but no rigid bodies are defined

#251 benmwebb closed 5 years ago
0
Use Python warnings module to report warnings

#250 benmwebb closed 5 years ago
0
Support hex colors in TopologyReader

#249 benmwebb closed 5 years ago
0
GaussianEMRestraint not selecting regions covered by pdb file when using TopologyReader

#248 grandrea closed 5 years ago
5
IMP.pmi.topology.TopologyReader does not process fasta_dir argument corretly

#247 tpeulen closed 5 years ago
1
Deleting fragment / beads from RMF in PMI 2.0

#246 ichem001 opened 6 years ago
1
Allow unambiguous inter-molecular crosslinks in restraints

#245 saltzberg opened 6 years ago
2
Make ProtocolOutput work with PMI2

#244 benmwebb closed 6 years ago
1
Fix GaussianEMRestraint to work with PMI2

#243 benmwebb closed 1 year ago
6
Fix the PMI2 tutorial

#242 benmwebb closed 6 years ago
1
Make a PMI1-only module

#241 benmwebb closed 6 years ago
3
Deprecate PMI1 classes

#240 benmwebb closed 5 years ago
1
Don't call Model.update() from restraint get_output() methods

#239 sethaxen closed 6 years ago
1
Add crosslink restraint to specific state

#238 ichem001 opened 6 years ago
0
Gaussian particles incorrectly placed by shuffle_configuration()

#237 benmwebb closed 6 years ago
6
Crosslinking restraint outputs take -log of score

#236 sethaxen closed 3 years ago
2
reading stat files was broken in f845cf26bd800569991b297a512a46f18099ce1f

#235 shanot closed 7 years ago
0
`IMP.pmi.tools.input_adaptor` does not return the leaves of the input hierarchies.

#234 Pellarin closed 7 years ago
2
ProcessOutput

#233 saltzberg opened 7 years ago
0
Rewrite ProcessOutput for speed and reliability

#232 saltzberg closed 7 years ago
1
Keep support for stat file v1?

#231 saltzberg closed 7 years ago
5
ProcessOutput is slow; don't use eval()

#230 saltzberg closed 1 year ago
2
Why is SerialMover used?

#229 sethaxen closed 7 years ago
4
tools.input_adaptor fails if the input list is empty

#228 Pellarin closed 7 years ago
0
Need a way to fix particles in pmi2.

#227 Pellarin closed 7 years ago
0
Create a test for tools.shuffle

#226 Pellarin closed 7 years ago
0
Add more optimizers to PMI and enable more choices wherever optimizers are used

#225 sethaxen closed 8 months ago
0
PMI2 RMF hierarchies of input and output RMFs different

#224 shruthivis opened 8 years ago
0
Add file prefix to mrc files

#223 shruthivis closed 1 year ago
1
Clustering function without stat file

#222 shruthivis opened 8 years ago
0
MPI number of cores problem for Analysis macro

#221 shruthivis opened 8 years ago
0
Add references to restraints

#220 sethaxen closed 8 months ago
0
Clustering and MPI: multiple copy of same models

#219 ichem001 opened 8 years ago
2
Set resolution in analysis replica exchange macro

#218 shruthivis opened 8 years ago
2
Connectivity for disordered proteins

#217 shruthivis closed 8 years ago
3
Port all systems to PMI2

#216 benmwebb closed 5 years ago
7
Merge ExternalBarrier and DistanceToPointRestraint restraints

#215 sethaxen closed 8 months ago
6