Improvements to ChimeraX 1.11.1
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you. Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
Maybe you are confusing two different programs: Chimera and ChimeraX. Each of those two programs has continuity of nearly all features, and we maintain backwards compatibility with its command syntax, but ONLY if you keep using the same program. Maybe you were using Chimera before and now you tried ChimeraX by mistake? Chimera still has the "Icosahedron Surface" tool, command "shape icosahedron" etc. For the two different programs, there are also two different websites, two different User Guides, two different email addresses for questions etc. Make sure you know what program you are using. <https://www.rbvi.ucsf.edu/chimerax/index.html> <https://www.rbvi.ucsf.edu/chimera/> 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 Feb 19, 2026, at 9:13 PM, Anindya Karmaker via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciat! e it if you would understand my frustration. Just my two cents. Thank you.
Sincerely, Anindya Karmaker ______________________________________ PhD Candidate, Chemical Engineering, UC Davis McDonald-Nandi Lab Email: akarmaker@ucdavis.edu Mobile: +1-530-760-8681, +880 1776929828 LinkedIn: _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Anindya, I think you are talking about differences between Chimera and ChimeraX. Those are two different programs. That is why features and command syntax differ. Here is a bit of history if you are interested. Chimera was developed from 1995 to 2015 and ChimeraX from 2015 to the present, both developed by the UCSF Computer Graphics Lab. We decided in 2015 that it was not sensible to continue Chimera development because it was based on 20-year old technologies, the Tk window toolkit and Python 2, and old OpenGL from before GPU shaders. So we opted to start a new program called ChimeraX based on the Qt window toolkit, Python 3 and modern OpenGL. Chimera was created over 20 years with 5 UCSF developers, and it was not feasible to reproduce that 100 person years of Chimera development in the new ChimeraX. Also we wanted to improve things that were not done well in Chimera for instance the way chains were specified in commands. Making a new program gave us an opportunity to fix things that could not be backward compatible. The result is that in the last 10 years ChimeraX has most of the useful old Chimera features but not all of them. And ChimeraX has many new advances such as AlphaFold, Boltz, and OpenFold structure prediction and dozens of other new capabilities that Chimera did not have. The UCSF Computer Graphics Lab has existed since the 1970s and made earlier molecular graphics programs. Before Chimera there was MidasPlus, before MidaPlus there was Midas. Before Midas I think there was one called MIDS. Each of these programs had a long life and then was replaced with a new program that kept the good features of the older program, added many new features, and broke compatibility to fix mistakes learned from a decade or more of use of the previous program. If there are specific features from Chimera that are not in ChimeraX that you like tell us on the mailing list. I'm not sure what you mean by the function "icosahedral"? There was an Icosahedral Cage GUI in Chimera and a "shape icosahedron" command and a related hkcage command. The Icosahedral Cage GUI is not in ChimeraX, the commands are in ChimeraX. I developed those Chimera capabilities. I liked the Icosahedral Cage GUI, but other capabilities such has machine learning structure prediction have had priority being more valuable to more people and I have not had time to recreate Isosahedral Cage in ChimeraX. We welcome outside developers making plugins for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/) and an Icosahedral Cage GUI would be easy for someone to contribute if they had the time and desire. Tom
On Feb 19, 2026, at 9:13 PM, Anindya Karmaker via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you.
Sincerely, Anindya Karmaker ______________________________________ PhD Candidate, Chemical Engineering, UC Davis McDonald-Nandi Lab Email: akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu> Mobile: +1-530-760-8681, +880 1776929828 LinkedIn: <https://www.linkedin.com/in/anindya-karmaker-943b66166/>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hello, I am sharing with you the screenshot of both ChimeraX 1.8 and ChimeraX 1.11.1 (NOT WORKING HERE). Same model same command. I am running on MacOS v26.3 [image: image.png] Best, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> On Fri, Feb 20, 2026 at 10:51 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Anindya,
I think you are talking about differences between Chimera and ChimeraX. Those are two different programs. That is why features and command syntax differ.
Here is a bit of history if you are interested. Chimera was developed from 1995 to 2015 and ChimeraX from 2015 to the present, both developed by the UCSF Computer Graphics Lab. We decided in 2015 that it was not sensible to continue Chimera development because it was based on 20-year old technologies, the Tk window toolkit and Python 2, and old OpenGL from before GPU shaders. So we opted to start a new program called ChimeraX based on the Qt window toolkit, Python 3 and modern OpenGL. Chimera was created over 20 years with 5 UCSF developers, and it was not feasible to reproduce that 100 person years of Chimera development in the new ChimeraX. Also we wanted to improve things that were not done well in Chimera for instance the way chains were specified in commands. Making a new program gave us an opportunity to fix things that could not be backward compatible. The result is that in the last 10 years ChimeraX has most of the useful old Chimera features but not all of them. And ChimeraX has many new advances such as AlphaFold, Boltz, and OpenFold structure prediction and dozens of other new capabilities that Chimera did not have. The UCSF Computer Graphics Lab has existed since the 1970s and made earlier molecular graphics programs. Before Chimera there was MidasPlus, before MidaPlus there was Midas. Before Midas I think there was one called MIDS. Each of these programs had a long life and then was replaced with a new program that kept the good features of the older program, added many new features, and broke compatibility to fix mistakes learned from a decade or more of use of the previous program.
If there are specific features from Chimera that are not in ChimeraX that you like tell us on the mailing list. I'm not sure what you mean by the function "icosahedral"? There was an Icosahedral Cage GUI in Chimera and a "shape icosahedron" command and a related hkcage command. The Icosahedral Cage GUI is not in ChimeraX, the commands are in ChimeraX. I developed those Chimera capabilities. I liked the Icosahedral Cage GUI, but other capabilities such has machine learning structure prediction have had priority being more valuable to more people and I have not had time to recreate Isosahedral Cage in ChimeraX. We welcome outside developers making plugins for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/) and an Icosahedral Cage GUI would be easy for someone to contribute if they had the time and desire.
Tom
On Feb 19, 2026, at 9:13 PM, Anindya Karmaker via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you.
Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear Tom, I am really thankful to UCSF team for building this amazing tool. It makes simulation and molecular modeling very easy to understand and explain. However, for my simple case, I just demonstrated the problem that I am facing. The proteins are not aligned hence the structures look very weird compared to viral capsids. But I just wanted to quickly point out the issue. I understand that it took many many years to make a software as good as this one and it takes years of dedicated people to get to this level. My comments are not to criticize but to understand if this was a design choice to replace this same function with a different command or why it is not working. Thank you. Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> On Fri, Feb 20, 2026 at 10:54 AM Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Hello, I am sharing with you the screenshot of both ChimeraX 1.8 and ChimeraX 1.11.1 (NOT WORKING HERE). Same model same command. I am running on MacOS v26.3 [image: image.png]
Best, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:51 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Anindya,
I think you are talking about differences between Chimera and ChimeraX. Those are two different programs. That is why features and command syntax differ.
Here is a bit of history if you are interested. Chimera was developed from 1995 to 2015 and ChimeraX from 2015 to the present, both developed by the UCSF Computer Graphics Lab. We decided in 2015 that it was not sensible to continue Chimera development because it was based on 20-year old technologies, the Tk window toolkit and Python 2, and old OpenGL from before GPU shaders. So we opted to start a new program called ChimeraX based on the Qt window toolkit, Python 3 and modern OpenGL. Chimera was created over 20 years with 5 UCSF developers, and it was not feasible to reproduce that 100 person years of Chimera development in the new ChimeraX. Also we wanted to improve things that were not done well in Chimera for instance the way chains were specified in commands. Making a new program gave us an opportunity to fix things that could not be backward compatible. The result is that in the last 10 years ChimeraX has most of the useful old Chimera features but not all of them. And ChimeraX has many new advances such as AlphaFold, Boltz, and OpenFold structure prediction and dozens of other new capabilities that Chimera did not have. The UCSF Computer Graphics Lab has existed since the 1970s and made earlier molecular graphics programs. Before Chimera there was MidasPlus, before MidaPlus there was Midas. Before Midas I think there was one called MIDS. Each of these programs had a long life and then was replaced with a new program that kept the good features of the older program, added many new features, and broke compatibility to fix mistakes learned from a decade or more of use of the previous program.
If there are specific features from Chimera that are not in ChimeraX that you like tell us on the mailing list. I'm not sure what you mean by the function "icosahedral"? There was an Icosahedral Cage GUI in Chimera and a "shape icosahedron" command and a related hkcage command. The Icosahedral Cage GUI is not in ChimeraX, the commands are in ChimeraX. I developed those Chimera capabilities. I liked the Icosahedral Cage GUI, but other capabilities such has machine learning structure prediction have had priority being more valuable to more people and I have not had time to recreate Isosahedral Cage in ChimeraX. We welcome outside developers making plugins for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/) and an Icosahedral Cage GUI would be easy for someone to contribute if they had the time and desire.
Tom
On Feb 19, 2026, at 9:13 PM, Anindya Karmaker via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you.
Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Anindya, Your sym command "sym #1 icoshedral" misspelled icosahedral, leaving out an "a" between the "s" and "h". Amazingly ChimeraX 1.8 accepted that. In fact ChimeraX 1.8 just looked at the first letter of the symmetry name, so the "i" and "sym #1 irresponsible" also gave 60 copies with no error message! But another user mistyped their symmetry command a few years ago and was not able to figure out what went wrong because of the ChimeraX 1.8 did not do very thorough error handling on the symmetry argument, so I improved that lax error handling so you actually have to type the symmetry name correctly. Here is my note on that fix https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15916#comment:2 Tom
On Feb 20, 2026, at 11:03 AM, Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Dear Tom, I am really thankful to UCSF team for building this amazing tool. It makes simulation and molecular modeling very easy to understand and explain. However, for my simple case, I just demonstrated the problem that I am facing. The proteins are not aligned hence the structures look very weird compared to viral capsids. But I just wanted to quickly point out the issue. I understand that it took many many years to make a software as good as this one and it takes years of dedicated people to get to this level.
My comments are not to criticize but to understand if this was a design choice to replace this same function with a different command or why it is not working. Thank you.
Sincerely, Anindya Karmaker ______________________________________ PhD Candidate, Chemical Engineering, UC Davis McDonald-Nandi Lab Email: akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu> Mobile: +1-530-760-8681, +880 1776929828 LinkedIn: <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:54 AM Anindya Karmaker <akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu>> wrote:
Hello, I am sharing with you the screenshot of both ChimeraX 1.8 and ChimeraX 1.11.1 (NOT WORKING HERE). Same model same command. I am running on MacOS v26.3 <image.png>
Best, Anindya Karmaker ______________________________________ PhD Candidate, Chemical Engineering, UC Davis McDonald-Nandi Lab Email: akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu> Mobile: +1-530-760-8681, +880 1776929828 LinkedIn: <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:51 AM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Anindya,
I think you are talking about differences between Chimera and ChimeraX. Those are two different programs. That is why features and command syntax differ.
Here is a bit of history if you are interested. Chimera was developed from 1995 to 2015 and ChimeraX from 2015 to the present, both developed by the UCSF Computer Graphics Lab. We decided in 2015 that it was not sensible to continue Chimera development because it was based on 20-year old technologies, the Tk window toolkit and Python 2, and old OpenGL from before GPU shaders. So we opted to start a new program called ChimeraX based on the Qt window toolkit, Python 3 and modern OpenGL. Chimera was created over 20 years with 5 UCSF developers, and it was not feasible to reproduce that 100 person years of Chimera development in the new ChimeraX. Also we wanted to improve things that were not done well in Chimera for instance the way chains were specified in commands. Making a new program gave us an opportunity to fix things that could not be backward compatible. The result is that in the last 10 years ChimeraX has most of the useful old Chimera features but not all of them. And ChimeraX has many new advances such as AlphaFold, Boltz, and OpenFold structure prediction and dozens of other new capabilities that Chimera did not have. The UCSF Computer Graphics Lab has existed since the 1970s and made earlier molecular graphics programs. Before Chimera there was MidasPlus, before MidaPlus there was Midas. Before Midas I think there was one called MIDS. Each of these programs had a long life and then was replaced with a new program that kept the good features of the older program, added many new features, and broke compatibility to fix mistakes learned from a decade or more of use of the previous program.
If there are specific features from Chimera that are not in ChimeraX that you like tell us on the mailing list. I'm not sure what you mean by the function "icosahedral"? There was an Icosahedral Cage GUI in Chimera and a "shape icosahedron" command and a related hkcage command. The Icosahedral Cage GUI is not in ChimeraX, the commands are in ChimeraX. I developed those Chimera capabilities. I liked the Icosahedral Cage GUI, but other capabilities such has machine learning structure prediction have had priority being more valuable to more people and I have not had time to recreate Isosahedral Cage in ChimeraX. We welcome outside developers making plugins for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/) and an Icosahedral Cage GUI would be easy for someone to contribute if they had the time and desire.
Tom
On Feb 19, 2026, at 9:13 PM, Anindya Karmaker via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you.
Sincerely, Anindya Karmaker ______________________________________ PhD Candidate, Chemical Engineering, UC Davis McDonald-Nandi Lab Email: akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu> Mobile: +1-530-760-8681, +880 1776929828 LinkedIn: <https://www.linkedin.com/in/anindya-karmaker-943b66166/>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Dear Tom, Thank you for clarifying. I just tried the corrected spelling. I may have mistyped it today to showcase the difference. But still in Chimera X1.11.1 on macOS 26.3 I am getting the same error. In Chimera X1.8 it works even with wrong spelling. [image: image.png] [image: image.png] Best, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> On Fri, Feb 20, 2026 at 11:17 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Anindya,
Your sym command "sym #1 icoshedral" misspelled icosahedral, leaving out an "a" between the "s" and "h". Amazingly ChimeraX 1.8 accepted that. In fact ChimeraX 1.8 just looked at the first letter of the symmetry name, so the "i" and "sym #1 irresponsible" also gave 60 copies with no error message! But another user mistyped their symmetry command a few years ago and was not able to figure out what went wrong because of the ChimeraX 1.8 did not do very thorough error handling on the symmetry argument, so I improved that lax error handling so you actually have to type the symmetry name correctly. Here is my note on that fix
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15916#comment:2
Tom
On Feb 20, 2026, at 11:03 AM, Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Dear Tom, I am really thankful to UCSF team for building this amazing tool. It makes simulation and molecular modeling very easy to understand and explain. However, for my simple case, I just demonstrated the problem that I am facing. The proteins are not aligned hence the structures look very weird compared to viral capsids. But I just wanted to quickly point out the issue. I understand that it took many many years to make a software as good as this one and it takes years of dedicated people to get to this level.
My comments are not to criticize but to understand if this was a design choice to replace this same function with a different command or why it is not working. Thank you.
Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:54 AM Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Hello, I am sharing with you the screenshot of both ChimeraX 1.8 and ChimeraX 1.11.1 (NOT WORKING HERE). Same model same command. I am running on MacOS v26.3 <image.png>
Best, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:51 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Anindya,
I think you are talking about differences between Chimera and ChimeraX. Those are two different programs. That is why features and command syntax differ.
Here is a bit of history if you are interested. Chimera was developed from 1995 to 2015 and ChimeraX from 2015 to the present, both developed by the UCSF Computer Graphics Lab. We decided in 2015 that it was not sensible to continue Chimera development because it was based on 20-year old technologies, the Tk window toolkit and Python 2, and old OpenGL from before GPU shaders. So we opted to start a new program called ChimeraX based on the Qt window toolkit, Python 3 and modern OpenGL. Chimera was created over 20 years with 5 UCSF developers, and it was not feasible to reproduce that 100 person years of Chimera development in the new ChimeraX. Also we wanted to improve things that were not done well in Chimera for instance the way chains were specified in commands. Making a new program gave us an opportunity to fix things that could not be backward compatible. The result is that in the last 10 years ChimeraX has most of the useful old Chimera features but not all of them. And ChimeraX has many new advances such as AlphaFold, Boltz, and OpenFold structure prediction and dozens of other new capabilities that Chimera did not have. The UCSF Computer Graphics Lab has existed since the 1970s and made earlier molecular graphics programs. Before Chimera there was MidasPlus, before MidaPlus there was Midas. Before Midas I think there was one called MIDS. Each of these programs had a long life and then was replaced with a new program that kept the good features of the older program, added many new features, and broke compatibility to fix mistakes learned from a decade or more of use of the previous program.
If there are specific features from Chimera that are not in ChimeraX that you like tell us on the mailing list. I'm not sure what you mean by the function "icosahedral"? There was an Icosahedral Cage GUI in Chimera and a "shape icosahedron" command and a related hkcage command. The Icosahedral Cage GUI is not in ChimeraX, the commands are in ChimeraX. I developed those Chimera capabilities. I liked the Icosahedral Cage GUI, but other capabilities such has machine learning structure prediction have had priority being more valuable to more people and I have not had time to recreate Isosahedral Cage in ChimeraX. We welcome outside developers making plugins for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/) and an Icosahedral Cage GUI would be easy for someone to contribute if they had the time and desire.
Tom
On Feb 19, 2026, at 9:13 PM, Anindya Karmaker via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you.
Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hey, I was curious so I tested this out on a 1.12 daily build. It looks like now it uses Schoenflies symbols for the point groups instead of names. `sym #1 I` worked, but `sym #1 icosahedral` did not. Best, Tony On Fri, Feb 20, 2026 at 12:17 PM Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Anindya,
Your sym command "sym #1 icoshedral" misspelled icosahedral, leaving out an "a" between the "s" and "h". Amazingly ChimeraX 1.8 accepted that. In fact ChimeraX 1.8 just looked at the first letter of the symmetry name, so the "i" and "sym #1 irresponsible" also gave 60 copies with no error message! But another user mistyped their symmetry command a few years ago and was not able to figure out what went wrong because of the ChimeraX 1.8 did not do very thorough error handling on the symmetry argument, so I improved that lax error handling so you actually have to type the symmetry name correctly. Here is my note on that fix
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15916#comment:2
Tom
On Feb 20, 2026, at 11:03 AM, Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Dear Tom, I am really thankful to UCSF team for building this amazing tool. It makes simulation and molecular modeling very easy to understand and explain. However, for my simple case, I just demonstrated the problem that I am facing. The proteins are not aligned hence the structures look very weird compared to viral capsids. But I just wanted to quickly point out the issue. I understand that it took many many years to make a software as good as this one and it takes years of dedicated people to get to this level.
My comments are not to criticize but to understand if this was a design choice to replace this same function with a different command or why it is not working. Thank you.
Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:54 AM Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Hello, I am sharing with you the screenshot of both ChimeraX 1.8 and ChimeraX 1.11.1 (NOT WORKING HERE). Same model same command. I am running on MacOS v26.3 <image.png>
Best, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:51 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Anindya,
I think you are talking about differences between Chimera and ChimeraX. Those are two different programs. That is why features and command syntax differ.
Here is a bit of history if you are interested. Chimera was developed from 1995 to 2015 and ChimeraX from 2015 to the present, both developed by the UCSF Computer Graphics Lab. We decided in 2015 that it was not sensible to continue Chimera development because it was based on 20-year old technologies, the Tk window toolkit and Python 2, and old OpenGL from before GPU shaders. So we opted to start a new program called ChimeraX based on the Qt window toolkit, Python 3 and modern OpenGL. Chimera was created over 20 years with 5 UCSF developers, and it was not feasible to reproduce that 100 person years of Chimera development in the new ChimeraX. Also we wanted to improve things that were not done well in Chimera for instance the way chains were specified in commands. Making a new program gave us an opportunity to fix things that could not be backward compatible. The result is that in the last 10 years ChimeraX has most of the useful old Chimera features but not all of them. And ChimeraX has many new advances such as AlphaFold, Boltz, and OpenFold structure prediction and dozens of other new capabilities that Chimera did not have. The UCSF Computer Graphics Lab has existed since the 1970s and made earlier molecular graphics programs. Before Chimera there was MidasPlus, before MidaPlus there was Midas. Before Midas I think there was one called MIDS. Each of these programs had a long life and then was replaced with a new program that kept the good features of the older program, added many new features, and broke compatibility to fix mistakes learned from a decade or more of use of the previous program.
If there are specific features from Chimera that are not in ChimeraX that you like tell us on the mailing list. I'm not sure what you mean by the function "icosahedral"? There was an Icosahedral Cage GUI in Chimera and a "shape icosahedron" command and a related hkcage command. The Icosahedral Cage GUI is not in ChimeraX, the commands are in ChimeraX. I developed those Chimera capabilities. I liked the Icosahedral Cage GUI, but other capabilities such has machine learning structure prediction have had priority being more valuable to more people and I have not had time to recreate Isosahedral Cage in ChimeraX. We welcome outside developers making plugins for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/) and an Icosahedral Cage GUI would be easy for someone to contribute if they had the time and desire.
Tom
On Feb 19, 2026, at 9:13 PM, Anindya Karmaker via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you.
Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you, Tom, for pointing that out. I will try this for future reference. Best, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> On Fri, Feb 20, 2026 at 11:50 AM Tony Schaefer <tony.schaefer.chem@gmail.com> wrote:
Hey,
I was curious so I tested this out on a 1.12 daily build. It looks like now it uses Schoenflies symbols for the point groups instead of names. `sym #1 I` worked, but `sym #1 icosahedral` did not.
Best,
Tony
On Fri, Feb 20, 2026 at 12:17 PM Tom Goddard via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Anindya,
Your sym command "sym #1 icoshedral" misspelled icosahedral, leaving out an "a" between the "s" and "h". Amazingly ChimeraX 1.8 accepted that. In fact ChimeraX 1.8 just looked at the first letter of the symmetry name, so the "i" and "sym #1 irresponsible" also gave 60 copies with no error message! But another user mistyped their symmetry command a few years ago and was not able to figure out what went wrong because of the ChimeraX 1.8 did not do very thorough error handling on the symmetry argument, so I improved that lax error handling so you actually have to type the symmetry name correctly. Here is my note on that fix
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15916#comment:2
Tom
On Feb 20, 2026, at 11:03 AM, Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Dear Tom, I am really thankful to UCSF team for building this amazing tool. It makes simulation and molecular modeling very easy to understand and explain. However, for my simple case, I just demonstrated the problem that I am facing. The proteins are not aligned hence the structures look very weird compared to viral capsids. But I just wanted to quickly point out the issue. I understand that it took many many years to make a software as good as this one and it takes years of dedicated people to get to this level.
My comments are not to criticize but to understand if this was a design choice to replace this same function with a different command or why it is not working. Thank you.
Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:54 AM Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Hello, I am sharing with you the screenshot of both ChimeraX 1.8 and ChimeraX 1.11.1 (NOT WORKING HERE). Same model same command. I am running on MacOS v26.3 <image.png>
Best, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:51 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Anindya,
I think you are talking about differences between Chimera and ChimeraX. Those are two different programs. That is why features and command syntax differ.
Here is a bit of history if you are interested. Chimera was developed from 1995 to 2015 and ChimeraX from 2015 to the present, both developed by the UCSF Computer Graphics Lab. We decided in 2015 that it was not sensible to continue Chimera development because it was based on 20-year old technologies, the Tk window toolkit and Python 2, and old OpenGL from before GPU shaders. So we opted to start a new program called ChimeraX based on the Qt window toolkit, Python 3 and modern OpenGL. Chimera was created over 20 years with 5 UCSF developers, and it was not feasible to reproduce that 100 person years of Chimera development in the new ChimeraX. Also we wanted to improve things that were not done well in Chimera for instance the way chains were specified in commands. Making a new program gave us an opportunity to fix things that could not be backward compatible. The result is that in the last 10 years ChimeraX has most of the useful old Chimera features but not all of them. And ChimeraX has many new advances such as AlphaFold, Boltz, and OpenFold structure prediction and dozens of other new capabilities that Chimera did not have. The UCSF Computer Graphics Lab has existed since the 1970s and made earlier molecular graphics programs. Before Chimera there was MidasPlus, before MidaPlus there was Midas. Before Midas I think there was one called MIDS. Each of these programs had a long life and then was replaced with a new program that kept the good features of the older program, added many new features, and broke compatibility to fix mistakes learned from a decade or more of use of the previous program.
If there are specific features from Chimera that are not in ChimeraX that you like tell us on the mailing list. I'm not sure what you mean by the function "icosahedral"? There was an Icosahedral Cage GUI in Chimera and a "shape icosahedron" command and a related hkcage command. The Icosahedral Cage GUI is not in ChimeraX, the commands are in ChimeraX. I developed those Chimera capabilities. I liked the Icosahedral Cage GUI, but other capabilities such has machine learning structure prediction have had priority being more valuable to more people and I have not had time to recreate Isosahedral Cage in ChimeraX. We welcome outside developers making plugins for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/) and an Icosahedral Cage GUI would be easy for someone to contribute if they had the time and desire.
Tom
On Feb 19, 2026, at 9:13 PM, Anindya Karmaker via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you.
Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Anindya, Oops! The correct syntax is "sym #1 i" or if you want to specify an coordinate system "sym #1 i,2n5". Always good to read the documentation (even if you are the one who wrote the code!). https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry Thorough documentation is one of the amazing features of ChimeraX. Tom
On Feb 20, 2026, at 11:44 AM, Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Dear Tom, Thank you for clarifying. I just tried the corrected spelling. I may have mistyped it today to showcase the difference. But still in Chimera X1.11.1 on macOS 26.3 I am getting the same error. In Chimera X1.8 it works even with wrong spelling. <image.png> <image.png>
Best, Anindya Karmaker ______________________________________ PhD Candidate, Chemical Engineering, UC Davis McDonald-Nandi Lab Email: akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu> Mobile: +1-530-760-8681, +880 1776929828 LinkedIn: <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 11:17 AM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Anindya,
Your sym command "sym #1 icoshedral" misspelled icosahedral, leaving out an "a" between the "s" and "h". Amazingly ChimeraX 1.8 accepted that. In fact ChimeraX 1.8 just looked at the first letter of the symmetry name, so the "i" and "sym #1 irresponsible" also gave 60 copies with no error message! But another user mistyped their symmetry command a few years ago and was not able to figure out what went wrong because of the ChimeraX 1.8 did not do very thorough error handling on the symmetry argument, so I improved that lax error handling so you actually have to type the symmetry name correctly. Here is my note on that fix
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15916#comment:2
Tom
On Feb 20, 2026, at 11:03 AM, Anindya Karmaker <akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu>> wrote:
Dear Tom, I am really thankful to UCSF team for building this amazing tool. It makes simulation and molecular modeling very easy to understand and explain. However, for my simple case, I just demonstrated the problem that I am facing. The proteins are not aligned hence the structures look very weird compared to viral capsids. But I just wanted to quickly point out the issue. I understand that it took many many years to make a software as good as this one and it takes years of dedicated people to get to this level.
My comments are not to criticize but to understand if this was a design choice to replace this same function with a different command or why it is not working. Thank you.
Sincerely, Anindya Karmaker ______________________________________ PhD Candidate, Chemical Engineering, UC Davis McDonald-Nandi Lab Email: akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu> Mobile: +1-530-760-8681, +880 1776929828 LinkedIn: <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:54 AM Anindya Karmaker <akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu>> wrote:
Hello, I am sharing with you the screenshot of both ChimeraX 1.8 and ChimeraX 1.11.1 (NOT WORKING HERE). Same model same command. I am running on MacOS v26.3 <image.png>
Best, Anindya Karmaker ______________________________________ PhD Candidate, Chemical Engineering, UC Davis McDonald-Nandi Lab Email: akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu> Mobile: +1-530-760-8681, +880 1776929828 LinkedIn: <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:51 AM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Anindya,
I think you are talking about differences between Chimera and ChimeraX. Those are two different programs. That is why features and command syntax differ.
Here is a bit of history if you are interested. Chimera was developed from 1995 to 2015 and ChimeraX from 2015 to the present, both developed by the UCSF Computer Graphics Lab. We decided in 2015 that it was not sensible to continue Chimera development because it was based on 20-year old technologies, the Tk window toolkit and Python 2, and old OpenGL from before GPU shaders. So we opted to start a new program called ChimeraX based on the Qt window toolkit, Python 3 and modern OpenGL. Chimera was created over 20 years with 5 UCSF developers, and it was not feasible to reproduce that 100 person years of Chimera development in the new ChimeraX. Also we wanted to improve things that were not done well in Chimera for instance the way chains were specified in commands. Making a new program gave us an opportunity to fix things that could not be backward compatible. The result is that in the last 10 years ChimeraX has most of the useful old Chimera features but not all of them. And ChimeraX has many new advances such as AlphaFold, Boltz, and OpenFold structure prediction and dozens of other new capabilities that Chimera did not have. The UCSF Computer Graphics Lab has existed since the 1970s and made earlier molecular graphics programs. Before Chimera there was MidasPlus, before MidaPlus there was Midas. Before Midas I think there was one called MIDS. Each of these programs had a long life and then was replaced with a new program that kept the good features of the older program, added many new features, and broke compatibility to fix mistakes learned from a decade or more of use of the previous program.
If there are specific features from Chimera that are not in ChimeraX that you like tell us on the mailing list. I'm not sure what you mean by the function "icosahedral"? There was an Icosahedral Cage GUI in Chimera and a "shape icosahedron" command and a related hkcage command. The Icosahedral Cage GUI is not in ChimeraX, the commands are in ChimeraX. I developed those Chimera capabilities. I liked the Icosahedral Cage GUI, but other capabilities such has machine learning structure prediction have had priority being more valuable to more people and I have not had time to recreate Isosahedral Cage in ChimeraX. We welcome outside developers making plugins for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/) and an Icosahedral Cage GUI would be easy for someone to contribute if they had the time and desire.
Tom
On Feb 19, 2026, at 9:13 PM, Anindya Karmaker via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you.
Sincerely, Anindya Karmaker ______________________________________ PhD Candidate, Chemical Engineering, UC Davis McDonald-Nandi Lab Email: akarmaker@ucdavis.edu <mailto:akarmaker@ucdavis.edu> Mobile: +1-530-760-8681, +880 1776929828 LinkedIn: <https://www.linkedin.com/in/anindya-karmaker-943b66166/>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thanks Tom. I usually have a good memory and try to use the same commands from my list and also have python scripts. But sure, I will probably use RAG to input the new manual and update my python scripts. Best, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> On Fri, Feb 20, 2026 at 11:55 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Anindya,
Oops! The correct syntax is "sym #1 i" or if you want to specify an coordinate system "sym #1 i,2n5". Always good to read the documentation (even if you are the one who wrote the code!).
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html#symmetry
Thorough documentation is one of the amazing features of ChimeraX.
Tom
On Feb 20, 2026, at 11:44 AM, Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Dear Tom, Thank you for clarifying. I just tried the corrected spelling. I may have mistyped it today to showcase the difference. But still in Chimera X1.11.1 on macOS 26.3 I am getting the same error. In Chimera X1.8 it works even with wrong spelling. <image.png> <image.png>
Best, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 11:17 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Anindya,
Your sym command "sym #1 icoshedral" misspelled icosahedral, leaving out an "a" between the "s" and "h". Amazingly ChimeraX 1.8 accepted that. In fact ChimeraX 1.8 just looked at the first letter of the symmetry name, so the "i" and "sym #1 irresponsible" also gave 60 copies with no error message! But another user mistyped their symmetry command a few years ago and was not able to figure out what went wrong because of the ChimeraX 1.8 did not do very thorough error handling on the symmetry argument, so I improved that lax error handling so you actually have to type the symmetry name correctly. Here is my note on that fix
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15916#comment:2
Tom
On Feb 20, 2026, at 11:03 AM, Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Dear Tom, I am really thankful to UCSF team for building this amazing tool. It makes simulation and molecular modeling very easy to understand and explain. However, for my simple case, I just demonstrated the problem that I am facing. The proteins are not aligned hence the structures look very weird compared to viral capsids. But I just wanted to quickly point out the issue. I understand that it took many many years to make a software as good as this one and it takes years of dedicated people to get to this level.
My comments are not to criticize but to understand if this was a design choice to replace this same function with a different command or why it is not working. Thank you.
Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:54 AM Anindya Karmaker <akarmaker@ucdavis.edu> wrote:
Hello, I am sharing with you the screenshot of both ChimeraX 1.8 and ChimeraX 1.11.1 (NOT WORKING HERE). Same model same command. I am running on MacOS v26.3 <image.png>
Best, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/>
On Fri, Feb 20, 2026 at 10:51 AM Tom Goddard <goddard@sonic.net> wrote:
Hi Anindya,
I think you are talking about differences between Chimera and ChimeraX. Those are two different programs. That is why features and command syntax differ.
Here is a bit of history if you are interested. Chimera was developed from 1995 to 2015 and ChimeraX from 2015 to the present, both developed by the UCSF Computer Graphics Lab. We decided in 2015 that it was not sensible to continue Chimera development because it was based on 20-year old technologies, the Tk window toolkit and Python 2, and old OpenGL from before GPU shaders. So we opted to start a new program called ChimeraX based on the Qt window toolkit, Python 3 and modern OpenGL. Chimera was created over 20 years with 5 UCSF developers, and it was not feasible to reproduce that 100 person years of Chimera development in the new ChimeraX. Also we wanted to improve things that were not done well in Chimera for instance the way chains were specified in commands. Making a new program gave us an opportunity to fix things that could not be backward compatible. The result is that in the last 10 years ChimeraX has most of the useful old Chimera features but not all of them. And ChimeraX has many new advances such as AlphaFold, Boltz, and OpenFold structure prediction and dozens of other new capabilities that Chimera did not have. The UCSF Computer Graphics Lab has existed since the 1970s and made earlier molecular graphics programs. Before Chimera there was MidasPlus, before MidaPlus there was Midas. Before Midas I think there was one called MIDS. Each of these programs had a long life and then was replaced with a new program that kept the good features of the older program, added many new features, and broke compatibility to fix mistakes learned from a decade or more of use of the previous program.
If there are specific features from Chimera that are not in ChimeraX that you like tell us on the mailing list. I'm not sure what you mean by the function "icosahedral"? There was an Icosahedral Cage GUI in Chimera and a "shape icosahedron" command and a related hkcage command. The Icosahedral Cage GUI is not in ChimeraX, the commands are in ChimeraX. I developed those Chimera capabilities. I liked the Icosahedral Cage GUI, but other capabilities such has machine learning structure prediction have had priority being more valuable to more people and I have not had time to recreate Isosahedral Cage in ChimeraX. We welcome outside developers making plugins for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/) and an Icosahedral Cage GUI would be easy for someone to contribute if they had the time and desire.
Tom
On Feb 19, 2026, at 9:13 PM, Anindya Karmaker via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a final year grad student at UCD and among many of my passions and recently acquired skills molecular biology/simulation is one of them. I have been using ChimeraX for some time now to learn and have used it extensively as well. But with every changing version I find wide gaps between functions.In the recent version 1.11.1 some commonly used functions like icoshedral have been completely removed and syntax changed. I develop applications for fun and utility as well and I understand that change is necessary. But you also have to understand backward compatibility. You simply cannot remove a function and expect people will adapt to it. Please do not remove syntax and backward compatibility. I understand that you may or may not be using AI to improve the application but one thing I found is that AI will hallucinate and will try to make changes or rewrite unnecessary code to prove its superiority which sometimes just removes backward compatibility. I would really appreciate it if you would understand my frustration. Just my two cents. Thank you.
Sincerely, *Anindya Karmaker* *______________________________________* *PhD Candidate, Chemical Engineering, UC Davis* *McDonald-Nandi Lab* *Email: **akarmaker@ucdavis.edu <akarmaker@ucdavis.edu>* *Mobile: **+1-530-760-8681, **+880 1776929828* *LinkedIn:* [image: Anindya Karmaker] <https://www.linkedin.com/in/anindya-karmaker-943b66166/> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (4)
-
Anindya Karmaker -
Elaine Meng -
Tom Goddard -
Tony Schaefer