Inquiry About Building Molecular Structures in ChimeraX
Dear Professor, I hope this message finds you well. I am currently engaged in machine learning research using ChimeraX. As part of my work, I need to substitute various groups on the phosphorus atom, including methyl, tert-butyl, cyano groups, and others. However, the current substitution function does not cover many groups, so I have been manually adding them to the SEQCROW library. At present, I am building the structures in Gaussian, which is quite cumbersome. Since I am not very familiar with ChimeraX, I am unsure whether it allows for manual molecular structure building. If such functionality is available, it would greatly assist my work. I would greatly appreciate any guidance or suggestions you might have. Thank you very much for your time and assistance. Best regards, Youcai Zhu 化工化工 1366924572@qq.com
Dear Youcai Zhu, See the Build Structure tool (menu: Tools... Structure Editing... Build Structure). You can click the Help button on this tool to see the help, or you can view the copy on our website: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> However, you may think that it is also cumbersome for building since it is step by step with many modifications. You could try it and see whether it is any easier for you than the methods you were already using. 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 2, 2024, at 6:27 AM, 化工化工 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Professor, I hope this message finds you well.
I am currently engaged in machine learning research using ChimeraX. As part of my work, I need to substitute various groups on the phosphorus atom, including methyl, tert-butyl, cyano groups, and others. However, the current substitution function does not cover many groups, so I have been manually adding them to the SEQCROW library.
At present, I am building the structures in Gaussian, which is quite cumbersome. Since I am not very familiar with ChimeraX, I am unsure whether it allows for manual molecular structure building. If such functionality is available, it would greatly assist my work.
I would greatly appreciate any guidance or suggestions you might have.
Thank you very much for your time and assistance.
Best regards, Youcai Zhu
Hello, I have a video on building and editing structures using seqcrow on youtube: https://www.youtube.com/watch?v=sBHr0Rz2ut4. Admittedly, building certain types of structures from scratch is not the easiest with seqcrow. Small organic molecules and coordination complexes with mono- or bidentate ligands are probably the easiest. Best, Tony Schaefer On Mon, Sep 2, 2024 at 9:51 AM Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Youcai Zhu, See the Build Structure tool (menu: Tools... Structure Editing... Build Structure).
You can click the Help button on this tool to see the help, or you can view the copy on our website: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html>
However, you may think that it is also cumbersome for building since it is step by step with many modifications. You could try it and see whether it is any easier for you than the methods you were already using.
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 2, 2024, at 6:27 AM, 化工化工 via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Professor, I hope this message finds you well.
I am currently engaged in machine learning research using ChimeraX. As part of my work, I need to substitute various groups on the phosphorus atom, including methyl, tert-butyl, cyano groups, and others. However, the current substitution function does not cover many groups, so I have been manually adding them to the SEQCROW library.
At present, I am building the structures in Gaussian, which is quite cumbersome. Since I am not very familiar with ChimeraX, I am unsure whether it allows for manual molecular structure building. If such functionality is available, it would greatly assist my work.
I would greatly appreciate any guidance or suggestions you might have.
Thank you very much for your time and assistance.
Best regards, Youcai Zhu
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participants (3)
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Elaine Meng -
Tony Schaefer -
化工化工