RosettaCommons/RFdiffusion issues and pull requests

#283 - Run error

Issue - State: open - Opened by zarbuk about 2 months ago - 1 comment

#282 - Gap-filling with RFdiffusion

Issue - State: closed - Opened by kjczarne about 2 months ago - 4 comments

#281 - bug

Issue - State: open - Opened by Ryosuke-254 about 2 months ago - 1 comment

#275 - Partial diffusion with sequences does not work

Issue - State: open - Opened by gezmi 2 months ago

#272 - Problem about design_ppi_scaffolded.sh in the example

Issue - State: open - Opened by kn301BE 3 months ago - 8 comments

#259 - Using sequence in potentials

Issue - State: closed - Opened by geraseva 4 months ago - 2 comments

#257 - FileNotFoundError:

Issue - State: open - Opened by Ryosuke-254 5 months ago - 3 comments

#256 - Installation doesn't recognize CUDA (due to numpy upgrade to v2.0.0)

Issue - State: open - Opened by harshagrawal13 5 months ago - 1 comment

#253 - use user HOME dir for cache, config, models

Pull Request - State: open - Opened by EricDeveaud 5 months ago - 1 comment

#241 - pyRosetta not found for Fold conditioning design

Issue - State: open - Opened by 363892878a 6 months ago - 3 comments

#238 - Traceback (most recent call last)

Issue - State: open - Opened by AIM132 6 months ago - 3 comments

#235 - curious to know whether only 3-helix binder protein could be design if using scaffold-based binder design.

Issue - State: open - Opened by Huilin-Li 6 months ago - 1 comment

#231 - RuntimeError: PytorchStreamReader failed reading zip archive: failed finding central directory

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

#227 - can't access http://files.ipd.uw.edu/pub/RFdiffusion/... to download weights

Issue - State: open - Opened by Huilin-Li 7 months ago - 3 comments

#221 - Issue with controlling motif scaffold length?

Issue - State: open - Opened by luiswyss 8 months ago - 1 comment

#214 - Partial diffusion errors

Issue - State: open - Opened by ibalafkir 8 months ago - 2 comments

#137 - How to use the trb file in combination with ProteinMPNN

Issue - State: open - Opened by wangdoc2002 about 1 year ago - 4 comments

#116 - CUDA not working

Issue - State: closed - Opened by ChengkuiZhao about 1 year ago

#115 - Got wrong Amino Acid

Issue - State: closed - Opened by ChengkuiZhao about 1 year ago - 6 comments

#115 - Got wrong Amino Acid

Issue - State: closed - Opened by ChengkuiZhao about 1 year ago - 6 comments

#114 - How to generate a binder when using Docker

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

#114 - How to generate a binder when using Docker

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

#113 - No pAE_interaction<10

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

#113 - No pAE_interaction<10

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

#111 - RuntimeError: cannot sample n_sample > prob_dist.size(-1) samples without replacement

Issue - State: open - Opened by spectral-flux about 1 year ago - 3 comments

#109 - ModuleNotFoundError: No module named 'pyrsistent'

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

#107 - Modifying Binder Length when using fold conditioning

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

#107 - Modifying Binder Length when using fold conditioning

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

#105 - Is it possible to run RFdiffusion without the GPU?

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

#105 - Is it possible to run RFdiffusion without the GPU?

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

#104 - How to do self-conditioning?

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

#103 - chain break doesn't work as expected

Issue - State: open - Opened by bzhousd over 1 year ago - 5 comments

#103 - chain break doesn't work as expected

Issue - State: open - Opened by bzhousd over 1 year ago - 5 comments

#102 - ProteinMPNN produces low-complexity result from RFDiffusion output

Issue - State: open - Opened by bwllc over 1 year ago

#101 - conda issue: ResolvePackageNotFound

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

#100 - 'no viable alternative at input' when designing binders

Issue - State: closed - Opened by jbrydon2 over 1 year ago - 5 comments

#100 - 'no viable alternative at input' when designing binders

Issue - State: closed - Opened by jbrydon2 over 1 year ago - 5 comments

#97 - Contigmap in Motif Scaffolding

Issue - State: open - Opened by plvdac1 over 1 year ago - 2 comments

#96 - Added p53 scaffolding example

Pull Request - State: closed - Opened by joewatchwell over 1 year ago

#96 - Added p53 scaffolding example

Pull Request - State: closed - Opened by joewatchwell over 1 year ago

#95 - Is conda a hard requirement?

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

#94 - Deep Learning Binder Results

Issue - State: open - Opened by okanders over 1 year ago - 10 comments

#93 - Using motif scaffolds for binder design

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

#91 - fine-tuning method

Issue - State: open - Opened by danboshuiyan over 1 year ago

#90 - Fixed incorrect variable name in contig parsing

Pull Request - State: closed - Opened by javierbq over 1 year ago

#89 - Adding p53 helix scaffold method to repository

Issue - State: closed - Opened by ttessie2 over 1 year ago - 1 comment

#89 - Adding p53 helix scaffold method to repository

Issue - State: closed - Opened by ttessie2 over 1 year ago - 1 comment

#88 - PAE interaction score

Issue - State: open - Opened by Najy-Yusuf over 1 year ago - 4 comments

#87 - Naming contigs in colab notebook

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

#86 - Using non-protein targets for binder design

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

#85 - Doubts regarding binder design results

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

#83 - updating rosetta-ci scripts to fix design_ppi_scaffolded test

Pull Request - State: closed - Opened by lyskov over 1 year ago - 1 comment

#82 - updating rosetta-ci scripts to fix design_ppi_scaffolded test

Pull Request - State: closed - Opened by lyskov over 1 year ago - 3 comments

#81 - Update install instructions for model directory location.

Pull Request - State: closed - Opened by roccomoretti over 1 year ago

#80 - Help with error: no such file or directory /models/Base_ckpt.pt

Issue - State: closed - Opened by ttessie2 over 1 year ago - 5 comments

#79 - OSError: [Errno 30] Read-only file system: 'outputs'

Issue - State: closed - Opened by maxh190 over 1 year ago - 1 comment

#79 - OSError: [Errno 30] Read-only file system: 'outputs'

Issue - State: closed - Opened by maxh190 over 1 year ago - 1 comment

#78 - I was installing RFdiffusion in my Linux system but ran into the following error.

Issue - State: closed - Opened by sHr3y4s1 over 1 year ago - 2 comments

#78 - I was installing RFdiffusion in my Linux system but ran into the following error.

Issue - State: closed - Opened by sHr3y4s1 over 1 year ago - 2 comments

#77 - FileNotFoundError: [Errno 2] No such file or directory: 'outputs/traj/test_0_pX0_traj.pdb'

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

#76 - How to design a dimer enzyme

Issue - State: closed - Opened by Lyang556 over 1 year ago - 2 comments

#74 - Symmetry mode NOT usable for e.g. inpainting a loop?

Issue - State: open - Opened by broomsday over 1 year ago

#74 - Symmetry mode NOT usable for e.g. inpainting a loop?

Issue - State: open - Opened by broomsday over 1 year ago

#72 - Swapped arguments when creating SymGen

Pull Request - State: closed - Opened by nzrandol over 1 year ago - 1 comment

#72 - Swapped arguments when creating SymGen

Pull Request - State: closed - Opened by nzrandol over 1 year ago - 1 comment

#71 - Implemented seed argument for reproducibility (redo)

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

#71 - Implemented seed argument for reproducibility (redo)

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

#70 - Implemented seed argument for reproducibility

Pull Request - State: closed - Opened by nzrandol over 1 year ago - 1 comment

#69 - N/A

Issue - State: closed - Opened by Bollzy over 1 year ago

#68 - Icosahedral symmetric oligomers?

Issue - State: open - Opened by evancollins1 over 1 year ago - 3 comments

#68 - Icosahedral symmetric oligomers?

Issue - State: open - Opened by evancollins1 over 1 year ago - 3 comments

#67 - Help: RFdiffusion EOFError: Ran out of input

Issue - State: closed - Opened by songhe2009 over 1 year ago - 1 comment

#67 - Help: RFdiffusion EOFError: Ran out of input

Issue - State: closed - Opened by songhe2009 over 1 year ago - 1 comment

#65 - Running RFdiffusion on Intel macbook pro without Nvidia GPU

Issue - State: open - Opened by shanghongsim over 1 year ago

#65 - Running RFdiffusion on Intel macbook pro without Nvidia GPU

Issue - State: open - Opened by shanghongsim over 1 year ago

#63 - Colabfold implementation

Issue - State: closed - Opened by ttessie2 over 1 year ago - 1 comment

#62 - partial diffusion with a few residues fixed

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

#62 - partial diffusion with a few residues fixed

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

#61 - Create a jupyter notebook

Issue - State: open - Opened by remybonnav over 1 year ago

#61 - Create a jupyter notebook

Issue - State: open - Opened by remybonnav over 1 year ago

#60 - Problem Hydra arguments on windows conda

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

#59 - download_models.sh : mkdir illegal option --

Pull Request - State: closed - Opened by tmsincomb over 1 year ago

#58 - adding integration with Rosetta CI

Pull Request - State: closed - Opened by lyskov over 1 year ago

#58 - adding integration with Rosetta CI

Pull Request - State: closed - Opened by lyskov over 1 year ago

#55 - Extend N-terminus with a helical bundle structure

Issue - State: closed - Opened by gha2012 over 1 year ago - 1 comment

#54 - Colab Error [Errno 2] No such file or directory: 'outputs/traj/test_0_pX0_traj.pdb'

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

#53 - Is it possible to use RFDiffusion for generating small molecule binders ?

Issue - State: closed - Opened by hima111997 over 1 year ago - 1 comment

#52 - Update Dockerfile to include icecream dependency

Pull Request - State: closed - Opened by gabi-a over 1 year ago

#51 - Finalize removing icecream as a dependency.

Pull Request - State: closed - Opened by roccomoretti over 1 year ago

#51 - Finalize removing icecream as a dependency.

Pull Request - State: closed - Opened by roccomoretti over 1 year ago

#49 - Enable discussions in Github repo

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

#49 - Enable discussions in Github repo

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

#48 - Ability to redesign existing scaffolds to create binding interfaces in comparison to de novo binder design

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

GitHub / RosettaCommons/RFdiffusion issues and pull requests