From 63decf556dc2cabfb679917b86d5f3a526a481e7 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Mon, 31 Jul 2023 11:18:07 +0200 Subject: [PATCH] Document that the MSA server is back to normal --- AlphaFold2.ipynb | 2 +- README.md | 9 ++++++--- batch/AlphaFold2_batch.ipynb | 2 +- 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/AlphaFold2.ipynb b/AlphaFold2.ipynb index 4b9f5757..b5d87666 100644 --- a/AlphaFold2.ipynb +++ b/AlphaFold2.ipynb @@ -57,7 +57,7 @@ "-----------\n", "\n", "### News\n", - "- 2023/07/27: ColabFold MSA server issue: We are using the backup server with old databases (UniRef30 2202/PDB70 220313) starting from ~8:30 AM CEST until we resolve the issue.\n", + "- 2023/07/31: The ColabFold MSA server is back to normal. It was using older DB (UniRef30 2202/PDB70 220313) from 27th ~8:30 AM CEST to 31st ~11:10 AM CEST.\n", "- 2023/06/12: New databases! UniRef30 updated to 2023_02 and PDB to 230517. We now use PDB100 instead of PDB70 (see [notes](#pdb100)).\n", "- 2023/06/12: We introduced a new default pairing strategy: Previously, for multimer predictions with more than 2 chains, we only pair if all sequences taxonomically match (\"complete\" pairing). The new default \"greedy\" strategy pairs any taxonomically matching subsets." ] diff --git a/README.md b/README.md index 68c694a5..c2f81b1f 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,8 @@ # ColabFold - v1.5.2 ```diff -- 27Jul2023: ColabFold MSA server issue: -- We are using the backup server with old databases -- (UniRef30 2202/PDB70 220313) starting from ~8:30 AM CEST until we resolve the issue. ++ 31Jul2023: 2023/07/31: The ColabFold MSA server is back to normal ++ It was using older DB (UniRef30 2202/PDB70 220313) from 27th ~8:30 AM CEST to 31st ~11:10 AM CEST. + 12Jun2023: New databases! UniRef30 updated to 2302 and PDB to 230517. + We now use PDB100 instead of PDB70 (see notes in the [main](https://colabfold.com) notebook). + 12Jun2023: We introduced a new default pairing strategy: @@ -138,6 +137,10 @@ Searches against the ColabFoldDB can be done in two different modes: ----------------- **OLD Updates** ```diff + 27Jul2023: ColabFold MSA server issue: + We are using the backup server with old databases + (UniRef30 2202/PDB70 220313) starting from ~8:30 AM CEST until we resolve the issue. + Resolved on 31Jul2023 ~11:10 CEST. 30Apr2023: Amber is working again in our ColabFold Notebook 29Apr2023: Amber is not working in our Notebook due to Colab update 18Feb2023: v1.5.2 - fixing: fixing memory leak for large proteins diff --git a/batch/AlphaFold2_batch.ipynb b/batch/AlphaFold2_batch.ipynb index 2fd782b5..de4e208f 100644 --- a/batch/AlphaFold2_batch.ipynb +++ b/batch/AlphaFold2_batch.ipynb @@ -56,7 +56,7 @@ "-----------\n", "\n", "### News\n", - "- 2023/07/27: ColabFold MSA server issue: We are using the backup server with old databases (UniRef30 2202/PDB70 220313) starting from ~8:30 AM CEST until we resolve the issue.\n", + "- 2023/07/31: The ColabFold MSA server is back to normal. It was using older DB (UniRef30 2202/PDB70 220313) from 27th ~8:30 AM CEST to 31st ~11:10 AM CEST.\n", "- 2023/06/12: New databases! UniRef30 updated to 2023_02 and PDB to 230517. We now use PDB100 instead of PDB70 (see notes in the [main](https://colabfold.com) notebook).\n", "- 2023/06/12: We introduced a new default pairing strategy: Previously, for multimer predictions with more than 2 chains, we only pair if all sequences taxonomically match (\"complete\" pairing). The new default \"greedy\" strategy pairs any taxonomically matching subsets." ]