Ecosyste.ms: Issues

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GitHub / deepmind/alphafold issues and pull requests

#813 - Oteri patch 1

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

#810 - Titin sequences causing alphafold warning and exit without result

Issue - State: open - Opened by dhan1004 over 1 year ago - 1 comment

#809 - Create SECURITY.md

Pull Request - State: open - Opened by gilbertalgordo over 1 year ago - 3 comments

#806 - ImageNotFound: 404 Client Error

Issue - State: open - Opened by beemo2 over 1 year ago

#805 - Unable to find image 'nvidia/cuda:11.0-base' locally

Issue - State: open - Opened by jimchen1551 over 1 year ago - 2 comments

#804 - list index out of range

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

#802 - Docker errors image not found

Issue - State: open - Opened by ikun821 over 1 year ago

#801 - --cpu and -cpu option not available from run_docker.py

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

#800 - Installing third-party software on alphafold colab not working

Issue - State: closed - Opened by songkim97 over 1 year ago - 1 comment

#799 - Colabfold import model error

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

#798 - conda and python compatibility

Issue - State: closed - Opened by YuriModeX over 1 year ago - 6 comments

#797 - Inconsistent Chain IDs in results

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

#796 - pLDDT in alphafold multimer

Issue - State: open - Opened by cclark1e over 1 year ago

#795 - AttributeError: module 'collections' has no attribute 'Iterable'

Issue - State: open - Opened by Ambrosia1224 over 1 year ago - 1 comment

#794 - how to calculate Neff

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

#793 - Where to Build Docker Image?

Issue - State: closed - Opened by dhan1004 over 1 year ago

#792 - ERROR when 'docker build -f docker/Dockerfile -t alphafold . '

Issue - State: open - Opened by lg10is1 over 1 year ago - 1 comment

#790 - Timing for MSA not reported/documented

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

#789 - max_template_date for Template-Free mode

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

#788 - Error in parsing custom template file

Issue - State: closed - Opened by data2code over 1 year ago - 2 comments
Labels: usage question

#787 - How to redownload the DB files?

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

#786 - How to run with 40 series cards

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

#785 - Request to change permissions requirements

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

#784 - Forcing known disulfide bridges to be formed

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

#783 - Random seed during inference

Issue - State: open - Opened by abhinavb22 over 1 year ago

#782 - Code didn't update to v3

Issue - State: open - Opened by mpm896 over 1 year ago - 2 comments

#781 - Alphafold 2.3.1+4 error while trying to build hexamer

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

#780 - Alphafold2 error

Issue - State: open - Opened by lmvl01 over 1 year ago - 2 comments

#779 - error

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

#778 - Jackhammer / stockholm.c "No space left on device"

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

#776 - Problems with my first run

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

#775 - alphafold2 doesn't work on RTX4090?

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

#774 - Download/Setup: FTP to HTTPS

Issue - State: closed - Opened by Faezov over 1 year ago - 1 comment
Labels: setup

#773 - Issues running alphafold with my script on local HPC

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

#772 - Uniref md5sum file has incorrect files

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

#771 - is alphafold using my GPU

Issue - State: open - Opened by Ahmedalaraby20 over 1 year ago - 6 comments

#770 - The official AlphaFold2-multimer package with non-docker.

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

#769 - pLLDT inconsistency between monomer and multimer

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

#766 - Max Templates Usage

Issue - State: open - Opened by mcale6 over 1 year ago

#765 - Attempting to run in AWS - not detecting GPU

Issue - State: open - Opened by rocketman8080 over 1 year ago

#764 - Cuda error appeared when I was running AlphaFold version >=2.2.4

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

#763 - invalid shape type=16

Issue - State: open - Opened by patrickbryant1 over 1 year ago

#762 - Colab AlphaFold.ipynb importing 'simtk.openmm' is deprecated error

Issue - State: closed - Opened by uvfulcrum over 1 year ago - 1 comment
Labels: colab

#761 - Function about MAP_HHBLITS_AATYPE_TO_OUR_AATYPE

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

#759 - TorsionAngleLoss in Algorithm 20 and 27

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

#757 - Alphafold-multimer fails trying to create features file

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

#755 - AlphaFold/Colab/RunTimeError

Issue - State: closed - Opened by incisrdg almost 2 years ago - 4 comments
Labels: colab

#754 - Change FTP server to a faster one

Pull Request - State: open - Opened by mprokhorov almost 2 years ago - 1 comment

#753 - Error with "common_modules.py

Issue - State: open - Opened by maaru1204 almost 2 years ago

#752 - Issue with mmCIF download through rsync

Issue - State: closed - Opened by alyhafez95 almost 2 years ago - 3 comments

#751 - Performance on network file system

Issue - State: closed - Opened by GlazerMann almost 2 years ago - 1 comment
Labels: third-party tool

#750 - unclear technical note on AlphaFold v2.3.0

Issue - State: open - Opened by RJ3 almost 2 years ago - 1 comment

#749 - running on A10/A40/A100 not working

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

#748 - Integrate Aim - an open-source experiment tracker

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

#747 - The program terminates after HHblits query runs for a while

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

#746 - Runtime Error with creating a dimer sequence

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

#744 - 2.3.2: update version number in setup.py

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

#743 - TypeError: tuple indices must be integers or slices, not str

Issue - State: open - Opened by DrJesseHansen almost 2 years ago - 1 comment

#742 - ptxas fatal : Ptx assembly aborted due to errors

Issue - State: open - Opened by DrJesseHansen almost 2 years ago - 1 comment

#741 - simtk.openmm.OpenMMException: Particle coordinate is nan

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

#740 - Out of GPU memory on A100 80GB

Issue - State: open - Opened by hypothalamus01 almost 2 years ago - 4 comments

#739 - comparing ready-made db vs. gsutil based download

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

#738 - Invalid resolution format: ['?']

Issue - State: closed - Opened by HF06 almost 2 years ago - 2 comments

#737 - no module named openmm

Issue - State: open - Opened by DrJesseHansen almost 2 years ago - 1 comment

#736 - third party tools run way too slow because of low cpu usage

Issue - State: closed - Opened by tq-kuaixu almost 2 years ago - 1 comment

#734 - AF Colab crashing

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

#731 - Using AlphaFold v 2.3.0 with older uniref30 DB?

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

#730 - Download script should fix permissions

Issue - State: open - Opened by bernt-matthias almost 2 years ago

#728 - update yinying's fork to official 2.3 release

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

#726 - Question regarding Alphafold2

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

#725 - Image Not found, pull access denied

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

#724 - bug: NAN in latest version of jax when using multimer+bfloat16

Issue - State: open - Opened by sokrypton almost 2 years ago - 4 comments

#722 - download_all_data.sh failed

Issue - State: open - Opened by kttn8769 almost 2 years ago - 1 comment

#721 - run model relaxation only?

Issue - State: open - Opened by nmrworker almost 2 years ago - 7 comments

#720 - Anybody succeeded running alphafold on AMD GPU?

Issue - State: open - Opened by saruarlive almost 2 years ago - 1 comment

#719 - Error when create a container

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

#718 - Zip result file is not written

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

#717 - What is the correct usage of "models_to_relax"?

Issue - State: closed - Opened by aravinda1879 almost 2 years ago - 1 comment

#715 - Bump Python to 3.9 in Colab

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

#714 - AlphaFold v2.3.1 Colab Notebook - ImportError: Python version mismatch

Issue - State: closed - Opened by biobrett6 almost 2 years ago - 4 comments
Labels: colab