Dear Dr. Elaine Yang,

I hope this message finds you well.

I am reaching out to seek your assistance regarding some issues I am facing with accessing certain resources. Specifically, the following links are not working: Protein-Ligand Binding Sites Tutorial: https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html ViewDockX Tool: https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html.

Additionally, I am unable to access any content from the ChimeraX tutorials. These resources are crucial for my current research, and I would greatly appreciate any help or guidance you can provide to resolve these issues.

Thank you very much for your time and assistance.

Best regards,

Ahmed Morsy

=========================

Ahmed Morsy, Ph.D.

Assistant Professor,

Department of Stem Cell & Regenerative Biotechnology,

Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea

Tel.: 02-450-0498

C.P.: +82/10-5299-5844

E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.kr

Orcid id: https://orcid.org/0000-0003-3873-9903

Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400)

Researchgate: https://www.researchgate.net/profile/Ahmed-Abdal-Dayem

GoogleScholar: https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en

On Saturday, June 15, 2024 at 12:39:01 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote:

UCSF ChimeraX version 1.8 has been released!

ChimeraX includes user documentation and is free for noncommercial use.

Download for Windows, Linux, and MacOS from:

https://www.rbvi.ucsf.edu/chimerax/download.html

Updates since version 1.7 (Dec 2023) include:

- show worm depictions of attribute values (B-factor, conservation, etc.)

using Render by Attribute tool or "cartoon byattribute" command

- show attribute values with atomic radii using Render by Attribute or

"size byattribute"

- Select by Attribute graphical interface

- Join Models generalized to any covalent bond (not just peptide)

- show multiple alternate locations simultaneously with "altlocs show"

- "pbond" command to create arbitrary pseudobonds

- "measure contactarea" to report the area of one surface within a cutoff

distance of another

- Segmentations tool for interactive manual segmentation in 2D slice views,

3D (desktop), or 3D (VR) can be applied to any volume data, not just

medical images; several fixes and ergonomic improvements including icons

to assign/deassign mouse and VR hand-controller modes with a single click

- set up and analyze batch AlphaFold predictions to search for

protein-protein interactions (commands for advanced users who can

run ColabFold directly on Linux)

support for:

- reading predicted aligned error (PAE) data from AlphaFold 3

- reading docking results from MOE

- fetching atomic structures and maps from PDB-REDO

- fetching/display of PDB NMR-STAR restraints

For details, please see the ChimeraX change log:

https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

On behalf of the team,

Elaine

-----

Elaine C. Meng, Ph.D.

UCSF Chimera(X) team

Resource for Biocomputing, Visualization, and Informatics

Department of Pharmaceutical Chemistry

University of California, San Francisco

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