From owner-chemistry@ccl.net Thu Jun 18 12:55:01 2020
From: "Raman Dutt rd650-,-snu.edu.in" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: Help required regarding the ChemNet Project
Message-Id: <-54107-200618121948-31793-dNnzoTfNwoe5beHa2IFJHw##server.ccl.net>
X-Original-From: "Raman  Dutt" <rd650 : snu.edu.in>
Date: Thu, 18 Jun 2020 12:19:46 -0400


Sent to CCL by: "Raman  Dutt" [rd650(a)snu.edu.in]
Dear All

I am a final-year student from India working on a project that requires 
replicating the ChemNet (https://arxiv.org/abs/1712.02734) experiment. 
Particularly, I want to know how to prepare the datasets such as Tox21 and 
chEMBL for multi-task classification. I am having some trouble in working with 
missing values in Tox21 and would be really grateful if someone could point me 
in a functional direction.

Warm Regards
Raman Dutt


From owner-chemistry@ccl.net Thu Jun 18 16:38:01 2020
From: "Elaine Meng meng.:.cgl.ucsf.edu" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL: UCSF ChimeraX version 1.0 release!
Message-Id: <-54108-200618163703-16537-q5tQvZ9/3t5wwdiVg9F/3Q:+:server.ccl.net>
X-Original-From: "Elaine  Meng" <meng*cgl.ucsf.edu>
Date: Thu, 18 Jun 2020 16:37:01 -0400


Sent to CCL by: "Elaine  Meng" [meng#%#cgl.ucsf.edu]
The UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI)
is pleased to announce the release of UCSF ChimeraX version 1.0!

ChimeraX includes full user documentation and is free for noncommercial use.
Download for Windows, Linux, and Mac OS X from: www.rbvi.ucsf.edu/chimerax/

Compared to Chimera, ChimeraX brings together:

(A) significant performance and graphics enhancements
 - interactive display of very large atomic structures and maps
 - interactive ambient-occlusion lighting and/or directional shadows
 - fast and robust molecular surfaces
 - fast mmCIF reader

(B) new implementations of Chimeras most highly used tools
 - map fitting, segmentation, volume eraser, volume filtering
 - morph maps or atomic structures
 - play back volume series or atomic trajectories
 - view ligand-receptor docking results
 - find H-bonds, find contacts and clashes
 - virtual mutation, amino acid sidechain rotamers
 - radial coloring, coloring by map value
 - coloring by molecular lipophilicity potential, B-factor, etc.
 - animatable 2D labels and arrows
 - shape command to draw spheres, cylinders, etc.
 - sequence viewer with sequence-structure crosstalk
 - interface to Modeller comparative modeling

(C) entirely new features
 - tube (curved cylinder) helices in cartoons
 - chain-chain contact diagram
 - H-bond or crosslink length histogram
 - built-in HTML browser with mechanism for click-to-execute commands

(D) support for new areas
 - virtual reality
 - light-sheet microscopy
 - medical imaging data

(E) major ease-of-use advances
 - toolbar with icons to perform actions with a single click
 - basic "undo"
 - more logical commands and more powerful command-line specification

(F) a web repository (ChimeraX Toolshed) for developers to contribute plugins