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, KoreaTel.: 02-450-0498C.P.: +82/10-5299-5844E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.krOrcid 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 _______________________________________________ ChimeraX-announce mailing list -- chimerax-announce@cgl.ucsf.edu To unsubscribe send an email to chimerax-announce-leave@cgl.ucsf.edu

Dear Dr. Elaine Meng, Thank you very much for the prompt response and solving the issue.I assure you that the sites are operating well. Have a nice day! Best regards,Ahmed =========================Ahmed Morsy, Ph.D. Department of Stem Cell & Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul05029, Korea C.P.: +82/10-5299-5844 E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.kr Orcidid: 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 Thursday, August 8, 2024 at 04:30:23 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Dr. Ahmed Morsy, The website and those links are working now.  Please try again -- sorry for the inconvenience. 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

On Aug 7, 2024, at 3:41 AM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:

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

Dear Ahmed Morsy, ChimeraX does have a Dock Prep tool, <https://rbvi.ucsf.edu/chimerax/docs/user/tools/dockprep.html> ...but it does not have general minimization, sorry, that is still work in progress. See the short list of features not yet in ChimeraX: <https://www.rbvi.ucsf.edu/chimerax/progress.html> There are some features in ChimeraX that can do a little minimization but it is not as complete as in Chimera. See: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html> There are dynamics in the ChimeraX ISOLDE plugin, but it may be for advanced users such as cryo-EM structural biologists. <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde> I hope this helps, 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

On Sep 6, 2024, at 8:01 PM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:

Dear Dr. Elaine,

Greetings!

I hope this message finds you well.

I would like to inquire if ChimeraX offers options for fixing PDB files, specifically for correcting hydrogen bonds and performing energy minimization, in preparation for docking studies.

I look forward to hearing from you and appreciate your guidance.

Best regards, Ahmed Morsy

Dear Dr. Elaine Meng,  I hope this message finds you well.  I would like to inquire if it is possible to calculate the RMSD value and TM-Score in ChimeraX to compare the differences between an experimental structure and an AlphaFold-predicted structure.  I look forward to your response. Best regards,Ahmed =========================Ahmed Morsy, Ph.D. Department of Stem Cell & Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul05029, Korea C.P.: +82/10-5299-5844 E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.kr Orcidid: 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, September 7, 2024 at 12:01:03 PM GMT+9, ahmed morsy <ahmed_morsy86@yahoo.com> wrote: Dear Dr. Elaine,  Greetings!  I hope this message finds you well.  I would like to inquire if ChimeraX offers options for fixing PDB files, specifically for correcting hydrogen bonds and performing energy minimization, in preparation for docking studies.  I look forward to hearing from you and appreciate your guidance.  Best regards,Ahmed Morsy =========================Ahmed Morsy, Ph.D. Department of Stem Cell & Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul05029, Korea C.P.: +82/10-5299-5844 E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.kr Orcidid: 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 Friday, August 9, 2024 at 04:13:02 PM GMT+9, ahmed morsy <ahmed_morsy86@yahoo.com> wrote: Dear Dr. Elaine Meng, Thank you very much for the prompt response and solving the issue.I assure you that the sites are operating well. Have a nice day! Best regards,Ahmed =========================Ahmed Morsy, Ph.D. Department of Stem Cell & Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul05029, Korea C.P.: +82/10-5299-5844 E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.kr Orcidid: 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 Thursday, August 8, 2024 at 04:30:23 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Dr. Ahmed Morsy, The website and those links are working now.  Please try again -- sorry for the inconvenience. 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

On Aug 7, 2024, at 3:41 AM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:

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

Dear Dr. Elaine, Thanks for your detailed reply.It's helpful. Have a nice weekend! Best regards,Ahmed ========================= Ahmed Morsy, Ph.D. Department of Stem Cell & Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul05029, Korea C.P.: +82/10-5299-5844 E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.kr Orcidid: 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 Friday, October 11, 2024 at 12:24:22 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Ahmed, ChimeraX does not calculate TM-Score.  You can calculate RMSD, but of course it depends on how the structures are superimposed.  The Matchmaker tool and command will do the superposition and also report an RMSD, but the fitting and RMSD only use the CA atoms that were paired by sequence alignment. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> If you need to use more atoms for superposition, see the "align" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> If  the structures are already superimposed, you can calculate RMSD over specified atoms using the "rmsd" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> I hope this helps, 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

On Oct 10, 2024, at 4:46 AM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:

Dear Dr. Elaine Meng,

I hope this message finds you well.

I would like to inquire if it is possible to calculate the RMSD value and TM-Score in ChimeraX to compare the differences between an experimental structure and an AlphaFold-predicted structure.

I look forward to your response.

Best regards, Ahmed

Dear Dr. Elaine, Greetings, I would like to ask if it is possible to use ChimeraX-predictable models for docking with small molecules.Are there precautions for that? Best regards,Ahmed =========================Ahmed Morsy, Ph.D. Department of Stem Cell & Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul05029, Korea C.P.: +82/10-5299-5844 E-mail: ahmed_morsy86@yahoo.com; ahmed@konkuk.ac.kr Orcidid: 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 _______________________________________________ ChimeraX-announce mailing list -- chimerax-announce@cgl.ucsf.edu To unsubscribe send an email to chimerax-announce-leave@cgl.ucsf.edu

Dear Dr. Elaine, Thanks for your detailed reply. It's helpful. Best regards, Ahmed On Monday, December 9, 2024 at 02:44:50 AM GMT+9, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmed, if you're asking whether ChimeraX predicts ligand-receptor binding modes, sorry, no it does not. If you are asking whether you can use the protein models from other modeling tools/programs to which ChimeraX has interfaces (Modeller, ESMFold, AlphaFold) for ligand-receptor docking, that is not anything that can be answered easily.  It depends on how much information was put into the modeling, how much is already known, etc., and how exactly you intend to interpret the results.  The bottom line is that you will have to rely on your own scientific judgement, including reading any published papers that have evaluated this issue.  These programs also provide their own "model scores" and some of them even have a per-residue pLDDT reliability score. See the help for each related tool/command in ChimeraX (and of course, you can do your own literature searches on these methods outside of ChimeraX): <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/esmfold.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> Regards, 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

On Dec 7, 2024, at 4:06 AM, ahmed morsy <ahmed_morsy86@yahoo.com> wrote:

Dear Dr. Elaine,

Greetings,

I would like to ask if it is possible to use ChimeraX-predictable models for docking with small molecules. Are there precautions for that?

Best regards, Ahmed