Ecosyste.ms: Issues

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GitHub / project-gemmi/gemmi issues and pull requests

#351 - Only printing header once in fprime program

Pull Request - State: closed - Opened by paulsbond 2 days ago

#350 - [Question] How to merge entities?

Issue - State: closed - Opened by lpravda 5 days ago - 4 comments

#349 - Entities don't get set up properly from a PHENIX refined model

Issue - State: closed - Opened by k-chrispens 23 days ago - 1 comment

#348 - CIF file created from Structure rejected by RCSB search portal

Issue - State: closed - Opened by jasondbiggs about 1 month ago - 1 comment

#346 - ItemPair conversion to ItemLoop

Issue - State: closed - Opened by cycle20 2 months ago - 1 comment

#345 - Solvent mask partial occ 202410

Pull Request - State: open - Opened by CV-GPhL 2 months ago - 3 comments

#344 - Slightly nicer (I think) formatting of a few items.

Pull Request - State: closed - Opened by CV-GPhL 2 months ago - 1 comment

#343 - FloatGrid resample_to missing?

Issue - State: closed - Opened by Dialpuri 2 months ago - 1 comment

#342 - Allow wider MODEL field to increase maximum number of models

Pull Request - State: closed - Opened by akors 3 months ago - 1 comment

#340 - Issue with find_nearest_pbc_position in Gemmi Neighbor Search

Issue - State: closed - Opened by MichalGucwa 3 months ago - 2 comments

#339 - calculating 1/d^2 is returning an array containing the same number.

Issue - State: closed - Opened by scatter3d 4 months ago - 4 comments

#338 - get_cra() ; with with typo

Pull Request - State: closed - Opened by MartinMalyMM 4 months ago - 1 comment

#336 - Crash when reading an mmjson file created by gemmi

Issue - State: closed - Opened by jasondbiggs 5 months ago - 1 comment

#335 - Add support for BinaryCIF

Issue - State: closed - Opened by jasondbiggs 5 months ago - 1 comment

#332 - pdbx_PDB_model_num type & content

Issue - State: closed - Opened by rimmartin 5 months ago - 2 comments

#332 - pdbx_PDB_model_num type & content

Issue - State: open - Opened by rimmartin 5 months ago - 2 comments

#331 - "gemmi convert" - HETNAM record

Issue - State: open - Opened by CV-GPhL 5 months ago - 8 comments

#331 - "gemmi convert" - HETNAM record

Issue - State: open - Opened by CV-GPhL 5 months ago - 2 comments

#330 - Segmentation Fault, Core Dumped

Issue - State: closed - Opened by m-crown 5 months ago - 9 comments

#330 - Segmentation Fault, Core Dumped

Issue - State: closed - Opened by m-crown 5 months ago - 9 comments

#329 - `gemmi.read_structure` fails to load some cif files from PDB-Dev

Issue - State: closed - Opened by NatureGeorge 6 months ago - 1 comment

#328 - compile error under ubuntu 24

Issue - State: closed - Opened by zhangfq-chemistry 6 months ago - 1 comment

#326 - Feature request: Gemmi alternative to 'NOISE' option of PDBSET

Issue - State: closed - Opened by drlemmus 7 months ago - 3 comments

#325 - PyMol saves mmCIF without auth_seq_id, fall back to label_seq_id

Pull Request - State: closed - Opened by milot-mirdita 7 months ago - 1 comment

#324 - [Feat] Ability to interpolate an array of coordinates

Pull Request - State: closed - Opened by jrobsontull 7 months ago - 4 comments

#323 - Interpolating many points in Python

Issue - State: closed - Opened by jrobsontull 7 months ago - 2 comments

#322 - Gemmi setup MapReorderOnly never sets AxisOrder for a grid

Issue - State: open - Opened by gabriellareggiano 7 months ago - 1 comment

#321 - -f <file> seems not to work as I expect

Issue - State: closed - Opened by KayDiederichs 8 months ago - 2 comments

#320 - Shared library is unversioned

Issue - State: closed - Opened by badshah400 8 months ago - 4 comments

#319 - Add Custom Boolean Check for Model Objects

Pull Request - State: closed - Opened by Dialpuri 8 months ago - 1 comment

#317 - Segfault when iterating over multiple structures

Issue - State: open - Opened by jackdent 9 months ago - 4 comments

#317 - Segfault when using the result of Chain.subchains()

Issue - State: closed - Opened by jackdent 9 months ago - 4 comments

#315 - Creating a structure from list of residues and their coordinates

Issue - State: closed - Opened by marinegor 9 months ago - 2 comments

#314 - [Question] bulk reading mmcif coordinates into a numpy array

Issue - State: closed - Opened by marinegor 9 months ago - 2 comments

#313 - [Bug Report] read_pdb mishandle the columns of extreme wild pdb files

Issue - State: closed - Opened by minhuanli 9 months ago - 5 comments

#311 - Advice to deal with AF3's broken CIF files

Issue - State: closed - Opened by milot-mirdita 9 months ago - 1 comment

#309 - pdb/cif entity subchain comparisons

Issue - State: closed - Opened by rimmartin 10 months ago - 1 comment

#308 - Bug in `get_all_unit_cell_sites()`

Issue - State: closed - Opened by fxcoudert 10 months ago - 5 comments

#307 - crash with set_extent

Issue - State: closed - Opened by JoshRackers 10 months ago - 4 comments

#306 - [FEATURE REQUEST] Add Python typing for `Vec3.__iter__`

Issue - State: closed - Opened by rjdirisio 10 months ago - 2 comments

#305 - Give the `Assembly` class a nicer string representation

Pull Request - State: closed - Opened by kalekundert 11 months ago - 1 comment

#303 - TER's effecting aligning

Issue - State: closed - Opened by rimmartin 11 months ago - 4 comments

#302 - sequence aligning with align_sequence_to_polymer

Issue - State: closed - Opened by rimmartin 11 months ago - 10 comments

#301 - Apparent sudden extra dependency for gemmi (zlib)

Issue - State: closed - Opened by helenginn 11 months ago - 5 comments

#299 - Missing _struct_ref_seq in cif generated from PDB without optional TER.

Issue - State: closed - Opened by xvlaurent 12 months ago - 2 comments

#297 - Segfault when importing `gemmi.cif`

Issue - State: closed - Opened by j-c-c 12 months ago - 2 comments

#296 - Uses of graph isomorphism and pynauty?

Issue - State: closed - Opened by j2kun 12 months ago - 2 comments

#295 - auto completion for gemmi grep

Issue - State: closed - Opened by frmupe about 1 year ago - 1 comment

#293 - python bindings: convert from pybind11 to nanobind, add type stubs

Issue - State: closed - Opened by wojdyr about 1 year ago - 1 comment

#292 - Vulnerability in `tinydir_file_open()`: buffer overflow

Issue - State: closed - Opened by merkys about 1 year ago - 2 comments

#291 - 1 test fails

Issue - State: closed - Opened by yurivict about 1 year ago - 1 comment

#290 - Issues with `gemmi::remove_ligands_and_waters`

Issue - State: closed - Opened by FilomenoSanchez about 1 year ago - 4 comments

#289 - Issue creating gemmi selections

Issue - State: closed - Opened by FilomenoSanchez about 1 year ago - 4 comments

#287 - Publishing PDB REMARK X's

Issue - State: closed - Opened by rimmartin about 1 year ago - 4 comments

#285 - False positive validation of a cif file with a missing category

Issue - State: closed - Opened by PeyratG over 1 year ago - 4 comments

#284 - OBSLTE from pdb and cif input

Issue - State: open - Opened by rimmartin over 1 year ago - 6 comments

#280 - C++ types in python docstrings

Issue - State: closed - Opened by sizmailov over 1 year ago - 2 comments

#278 - Enhancement: Extend Python API to Support --nfree Argument Functionality

Issue - State: closed - Opened by vivek8031 over 1 year ago - 1 comment

#277 - What CIF data gets used to generate symmetry mates?

Issue - State: closed - Opened by ljmartin over 1 year ago - 2 comments

#275 - Linking issue using conda-forge package of gemmi on linux

Issue - State: closed - Opened by agrossfield over 1 year ago - 3 comments

#274 - publishing CONECT records

Pull Request - State: closed - Opened by rimmartin over 1 year ago - 2 comments

#273 - The defining of preprocessor CHECK collides with unit test software

Issue - State: closed - Opened by rimmartin over 1 year ago - 2 comments

#272 - Inconsistency in mtz labels in sf2mtz and then sf2map (DELPHWT vs PHDELWT)

Issue - State: closed - Opened by epeisach over 1 year ago - 2 comments

#271 - Several warnings when compiling with nvcc

Issue - State: closed - Opened by correaa over 1 year ago - 4 comments

#270 - [FEATURE REQUEST] set types to type_energy in chem comp output

Issue - State: closed - Opened by rimmartin over 1 year ago - 1 comment

#269 - [FEATURE REQUEST] initial data_comp_list section in ChemComp output

Issue - State: open - Opened by rimmartin over 1 year ago - 3 comments

#268 - Fails to build with GCC 13

Issue - State: closed - Opened by merkys over 1 year ago - 4 comments

#267 - [FEATURE REQUEST] put x, y, z columns in chemcomp _chem_comp_atom loop

Issue - State: closed - Opened by rimmartin over 1 year ago - 5 comments

#265 - write Chemical Component to cif file

Issue - State: closed - Opened by rimmartin over 1 year ago - 4 comments

#264 - Fix compilation with GCC 13

Pull Request - State: closed - Opened by krab1k almost 2 years ago - 1 comment

#263 - Normalize in sf2map isn't normalizing?

Issue - State: closed - Opened by pschmidtke almost 2 years ago - 3 comments

#262 - Building a document from a chain in C++

Issue - State: closed - Opened by dcelisgarza almost 2 years ago - 2 comments

#261 - Feature request for cif2mtz

Issue - State: closed - Opened by CV-GPhL almost 2 years ago - 6 comments

#260 - xds2mtz: New option --batchmin to delete batches with BATCH<BATCHMIN Default 1.

Pull Request - State: closed - Opened by githubgphl almost 2 years ago - 2 comments

#259 - Since v0.6.0 cannot "import gemmi"

Issue - State: closed - Opened by neumannrf almost 2 years ago - 7 comments

#258 - [FEATURE REQUEST] make gemmi.cif.Block object picklable

Issue - State: closed - Opened by roshkjr almost 2 years ago - 10 comments
Labels: low-priority

#257 - How to build the C++ library separately, and the Python library separately?

Issue - State: closed - Opened by yurivict almost 2 years ago - 4 comments

#256 - xds2mtz fixup reading XDS_ASCII.HKL that does not have MAXC column.

Pull Request - State: closed - Opened by githubgphl almost 2 years ago - 1 comment

#255 - Xds2mtz add on

Pull Request - State: closed - Opened by githubgphl almost 2 years ago - 2 comments

#253 - Example for parsing a cif file from RCSB to a protein file and a ligand file

Issue - State: closed - Opened by KSUN63 almost 2 years ago - 5 comments

#252 - Gemmi failing to process large? entry 5j7v

Issue - State: closed - Opened by otienoanyango almost 2 years ago - 6 comments

#251 - cif Block, erase certain columns

Issue - State: closed - Opened by richardjgowers almost 2 years ago - 2 comments

#250 - replaced cpp warning directive with pragma message

Pull Request - State: closed - Opened by MergunFrimen about 2 years ago - 4 comments

#249 - Provide type information for Python

Issue - State: closed - Opened by eggplants about 2 years ago - 4 comments
Labels: low-priority

#247 - Update cif.Style.Pdbx to write aligned columns and formatted pairs values

Issue - State: closed - Opened by roshkjr about 2 years ago - 5 comments

#246 - Pip install doesn't work

Issue - State: closed - Opened by drorhunvural about 2 years ago - 4 comments

#245 - python: added contains operator to cif.Document

Pull Request - State: closed - Opened by richardjgowers about 2 years ago - 1 comment

#244 - incorrect assembly formed by gemmi compared to RCSB

Issue - State: closed - Opened by danny305 about 2 years ago - 1 comment

#243 - orthorhombic maps lose periodic boundary conditions in P1

Issue - State: closed - Opened by dennisbrookner about 2 years ago - 4 comments

#242 - gemmi cif2mtz and wavelength issue?

Issue - State: closed - Opened by CV-GPhL about 2 years ago - 10 comments