Changes between Version 47 and Version 48 of NTTData

Timestamp:

Aug 27, 2021, 12:42:25 PM (4 years ago)

Author:

Elaine Meng

Comment:

--

NTTData

@@ -325 +325 @@
 Phil: a cautionary tale is progesterone receptor 1a28 alphafold match, you can see that multiple domains even within a monomer chain are not placed as expected relative to each other.
 
+== 8/11/2021 ==
+
+Phil, Philip, Darrell (last 15 mins); Elaine, Eric, TomG, Zach, Scooter
+
+Philip: NIH3D pipeline is progressing, uses ChimeraX pubchem and EMDB fetch, mostly working well. Sent recent error message in chat for Eric to take a look.
+
+Phil: found out your system was down when trying to file a ChimeraX bug report, that swapaa does not change sequence in Sequence Viewer. It's on Eric's todo list.
+
+TomG: screenshare demo: uniprot features, alphafold GUI. Fetch (alphafold match) and AlphaFold Coloring panel. Corresponding commands show alphafold-generated residue attributes. Many options apply only when there is a corresponding experimental chain, will be grayed out. Search (alphafold search) runs blastprotein on the alphafold database. Predict (alphafold predict) runs Google Colab version of alphafold.
+
+Will show warning that this notebook is from github (was not authored by Google); click button to run anyway. Requires Google account and initial sign-in. Sign-in may be retained by cookies depending on your browser settings. Next, HMMER, AlphaFold, and OpenMM are installed on a virtual machine. Then sequence databases are searched, a multiple sequence alignment generated, and the structure predicted. The entire process typically takes on the order of an hour or more.