Ecosyste.ms: Issues

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GitHub / RosettaCommons/RoseTTAFold issues and pull requests

#138 - Cuda11 compatibility

Issue - State: open - Opened by rmarabini about 1 year ago

#137 - Bus error (core dumped) while running predict_e2e.py

Issue - State: open - Opened by michaelhsieh42 about 1 year ago

#136 - Is there something way to run without conda?

Issue - State: open - Opened by darkcircle about 1 year ago

#134 - the content of decompressed database file

Issue - State: open - Opened by lgw2023 over 1 year ago - 1 comment

#133 - RFdiffusion

Issue - State: open - Opened by donglg1309 over 1 year ago - 2 comments

#132 - Unzipped database sizes?

Issue - State: open - Opened by KirkDSL over 1 year ago - 2 comments

#131 - fix typo in modules.py

Pull Request - State: open - Opened by eltociear over 1 year ago

#130 - Does the rosettafold can be installed in arm computers?

Issue - State: open - Opened by liuyong201811 almost 2 years ago

#129 - From heat maps/coordinates to folded protein structures.

Issue - State: closed - Opened by WikGitHub almost 2 years ago

#128 - MSAs from AlphaFold

Issue - State: open - Opened by almeida85 almost 2 years ago

#127 - [Question] Is Linux ARM64 supported ?

Issue - State: open - Opened by gancho-ivanov almost 2 years ago - 2 comments

#126 - [make_msa] ERROR

Issue - State: open - Opened by oghzzang almost 2 years ago

#125 - fix permission errors on shared file systems

Pull Request - State: open - Opened by zemu-unile almost 2 years ago

#124 - "ERROR: failed to load model" for complex-modeling

Issue - State: open - Opened by munmunbhasin almost 2 years ago - 2 comments

#122 - Untarring pdb100_2021Mar03.tar.gz

Issue - State: open - Opened by tekpinar about 2 years ago - 3 comments

#121 - How to find some introductions about these packages?

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

#120 - File permissions error when running on shared filesystem

Issue - State: open - Opened by james-vincent about 2 years ago - 2 comments

#119 - How to use Rosetta online?

Issue - State: closed - Opened by HectorTo about 2 years ago

#117 - Predicting PPI on homodimer

Issue - State: open - Opened by what-is-what about 2 years ago

#116 - Activating conda environments

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

#115 - realpath: missing operand - running the run_[pyrosetta, e2e]_ver.sh

Issue - State: open - Opened by siupenyau about 2 years ago - 1 comment

#114 - Getopt

Pull Request - State: open - Opened by ghbhc over 2 years ago

#113 - hhsearch can't running

Issue - State: closed - Opened by zliu36 over 2 years ago

#112 - PPI screening output file (*.npz)

Issue - State: open - Opened by Kaixiang-Wang over 2 years ago - 2 comments

#111 - network_2tracker with pdb

Issue - State: open - Opened by Lsz-20 over 2 years ago

#110 - search_msa database sequencing

Pull Request - State: closed - Opened by shawncal over 2 years ago - 1 comment

#109 - add dockerfile and dronefile

Pull Request - State: closed - Opened by hmc-cs-bbaker over 2 years ago

#108 - missing file in pdb100_2021Mar03.tar.gz

Issue - State: closed - Opened by abotzki over 2 years ago - 2 comments

#107 - ValueError: Number of processes must be at least 1

Issue - State: open - Opened by francicco over 2 years ago - 2 comments

#106 - the disitance bin

Issue - State: open - Opened by jsr2222 over 2 years ago - 1 comment

#105 - with cuda 10.1 Pytorch says that CUDA is not available

Issue - State: open - Opened by napoler over 2 years ago

#103 - predict protein ligand binding site and do molecular docking

Issue - State: open - Opened by heeqee over 2 years ago

#101 - How to use 2 track network?

Issue - State: closed - Opened by what-is-what over 2 years ago - 7 comments

#100 - RoseTTAFold e2e generate wrong pdb

Issue - State: closed - Opened by hartrials over 2 years ago

#99 - generate eukaryotes paired alignments file in complex-modeling

Issue - State: open - Opened by luuululu over 2 years ago - 3 comments

#98 - Add Docker container image that is also compatible with Singularity

Pull Request - State: open - Opened by javierbq over 2 years ago

#97 - Scripts to build pdb100

Issue - State: open - Opened by balvisio over 2 years ago

#96 - IndexError: list index out of range

Issue - State: closed - Opened by Wud1 over 2 years ago - 2 comments

#95 - Predict in batch mode

Issue - State: open - Opened by tomer196 over 2 years ago

#93 - $PIPEDIR/network/predict_pyRosetta.py

Issue - State: open - Opened by jennifermbui over 2 years ago - 4 comments

#92 - can anyone setup RoseTTAFold on Google Colab?

Issue - State: open - Opened by GeorvityLabs over 2 years ago - 5 comments

#91 - generating the complex template npz file

Issue - State: open - Opened by mukhyala over 2 years ago

#90 - Predict sequences with non-natural amino acids

Issue - State: open - Opened by ichxw almost 3 years ago

#89 - Refine_module xyz.detach()

Issue - State: open - Opened by esun0087 almost 3 years ago

#88 - UnsatisfiableError during installation of RosettaFold

Issue - State: open - Opened by Sunyp-IM almost 3 years ago - 3 comments

#87 - something about mirror image

Issue - State: open - Opened by esun0087 almost 3 years ago

#86 - failed to predict distance and orientation

Issue - State: open - Opened by jennifermbui almost 3 years ago

#85 - pyrosetta complains about pyhton versione in conda environment folding

Issue - State: open - Opened by renato-lombardo almost 3 years ago - 4 comments

#84 - How to train the RoseTTAFold

Issue - State: open - Opened by wuwo007 almost 3 years ago - 4 comments

#83 - Complex Structure Modelling invalid syntax

Issue - State: open - Opened by aputron almost 3 years ago

#82 - Segmentation fault problem (could not open file)

Issue - State: open - Opened by NikoBelice almost 3 years ago - 1 comment

#81 - Error: Unrecognized HMM file format in '1507521083'

Issue - State: open - Opened by A-Talavera almost 3 years ago - 2 comments

#80 - Run run_pyrosetta_ver.sh, Internal: Blas SGEMM launch failed

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

#79 - failed hhsearch

Issue - State: closed - Opened by jessu10 almost 3 years ago - 6 comments

#78 - Which version of TensorFlow？

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

#77 - GLY-ALA ----> ALA-GLY

Issue - State: closed - Opened by pguillem almost 3 years ago - 1 comment

#76 - msa and network issues

Issue - State: open - Opened by adxyzz almost 3 years ago - 3 comments

#75 - "out of memory" on multi-GPU platform

Issue - State: closed - Opened by IvanWoo22 almost 3 years ago - 16 comments

#74 - segmentation fault at make_msa.sh

Issue - State: open - Opened by yoavatsmonraz almost 3 years ago - 4 comments

#73 - Complex example: CUDA out of memory

Issue - State: open - Opened by chenyuwai almost 3 years ago - 2 comments

#72 - Estogram Calculation

Issue - State: closed - Opened by what-is-what almost 3 years ago - 1 comment

#71 - RoseTTAFold/DAN-msa/models/smTr_rep1/ checkpoint files

Issue - State: open - Opened by callahak almost 3 years ago

#70 - Example/pyrosetta/log/folding.stderr - No moduled named 'pyrosetta'

Issue - State: closed - Opened by what-is-what almost 3 years ago - 7 comments

#69 - cat make_msa.stderr

Issue - State: open - Opened by Niohuruzh almost 3 years ago - 3 comments

#68 - ERROR: sequence ss_pred contains no residues.

Issue - State: open - Opened by 1000000000000000000000000000000 almost 3 years ago - 25 comments

#67 - Issues on shared system - file permission

Issue - State: closed - Opened by Sabryr almost 3 years ago - 8 comments

#66 - "sequence ss_pred contains no residues."when running hhsearch

Issue - State: closed - Opened by Meowooo almost 3 years ago - 4 comments

#65 - "sequence ss_pred contains no residues.

Issue - State: open - Opened by Meowooo almost 3 years ago - 1 comment

#64 - Run hhsearch have not "t000_.atab"

Issue - State: open - Opened by Meowooo almost 3 years ago - 2 comments

#63 - Run example, ModelQ.dat show about 0.27

Issue - State: open - Opened by ChrisLou-bioinfo almost 3 years ago - 5 comments

#62 - lddt folder problem

Issue - State: closed - Opened by luckydogomg almost 3 years ago - 1 comment

#61 - predict short fragment ERROR

Issue - State: open - Opened by pfreezer almost 3 years ago - 1 comment

#60 - there is no t000_.e2e.pdb

Issue - State: open - Opened by winkingonly almost 3 years ago - 6 comments

#59 - Unable to download the weights dataset

Issue - State: open - Opened by sayaneshome almost 3 years ago - 2 comments

#58 - ValueError: Number of processes must be at least 1

Issue - State: open - Opened by Rusfell almost 3 years ago

#57 - Ask for help when predicting thousands of proteins

Issue - State: open - Opened by Rusfell almost 3 years ago - 1 comment

#55 - CUDA kernel errors

Issue - State: open - Opened by jong3 almost 3 years ago - 2 comments

#54 - No GPU available

Issue - State: closed - Opened by Rusfell almost 3 years ago - 1 comment

#53 - Update predict_complex README

Pull Request - State: closed - Opened by neilfleckSCRI almost 3 years ago - 3 comments

#51 - Don't gain model folder.

Issue - State: open - Opened by lll16 almost 3 years ago - 2 comments

#50 - no pdb outcome in the pyrosetta run version

Issue - State: open - Opened by ajian-he almost 3 years ago - 6 comments

#46 - Cuda out of memory error

Issue - State: open - Opened by ryao-mdanderson almost 3 years ago - 5 comments

#45 - Is the md5 hash for the database files available?

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

#42 - CUDA error help

Issue - State: open - Opened by Wenzhe-Ma almost 3 years ago - 2 comments

#39 - Issue with running hhsearch to completion

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

#32 - realpath: missing operand

Issue - State: closed - Opened by chenliuqing1990 almost 3 years ago - 1 comment

#30 - Can it work on Windows?

Issue - State: closed - Opened by ZhaoPengpeng1116 almost 3 years ago - 4 comments

#27 - Example for more-than-2-proteins complex estimation

Issue - State: open - Opened by andreasntr almost 3 years ago - 3 comments

#20 - error in Install

Issue - State: open - Opened by lll16 almost 3 years ago - 5 comments

#18 - Results on CASP14 targets

Issue - State: open - Opened by jiaxiang-wu almost 3 years ago - 5 comments

#13 - "buffer overflow detected" when using psipred.

Issue - State: open - Opened by panganqi almost 3 years ago - 21 comments

#9 - Running predictions for Protein-Protein complexes

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

#3 - PDB100 database compatability issues

Issue - State: closed - Opened by martin-steinegger almost 3 years ago - 4 comments