Assistance Required: Extracting List of Interacting Residues within 4 Å in UCSF Chimera
Dear UCSF Chimera Support Team, I hope this message finds you well. I am currently working on analyzing interactions between two molecular structures using UCSF Chimera. I have successfully identified residues that are within a 4 Å distance between the two molecules. However, I am encountering difficulties in obtaining a clear, textual list of these interacting residues, as reading them directly from the visual representation is challenging. Could you please provide guidance on the specific commands or procedures within Chimera that would allow me to: 1. *Select residues* in one molecule that are within 4 Å of the other molecule. 2. *Generate and export a list* of these selected residues for further analysis. I have attempted various selection and reporting commands but have not yet achieved the desired outcome. Detailed instructions or references to relevant documentation would be greatly appreciated. Thank you very much for your assistance. Best regards, Rashmi
Hi Rashmi, I can't give the specific commands for your project since you didn't give specific information: I don't know if these molecules are in different models, or different chains in the same model, and whether they also contain other chains and/or molecules like water and ligands. So I can only describe things generally. The general approach is to select the nearby residues and then use the info command to write a list of the selection. (1) Selecting the residues. There are lots of ways to select the nearby residues, either using the menu/GUIs or commands. The menus/GUIs might be easier if you are a beginner. For the mostly-menu approach, you'd first select one molecule (with Select menu or "select" command), and then use menu: Select... Zone. For the command approach, see "select zone" help and examples therein: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#zone> (2) Listing the selection. You can use command info residues sel ... just to show it in the Log, or to save it to a text file, for example ~/Desktop/residues.txt, use another option: info residues sel saveFile ~/Desktop/residues.txt see "info residues" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 27, 2025, at 8:26 AM, Rashmi Aggarwal via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF Chimera Support Team, I hope this message finds you well. I am currently working on analyzing interactions between two molecular structures using UCSF Chimera. I have successfully identified residues that are within a 4 Å distance between the two molecules. However, I am encountering difficulties in obtaining a clear, textual list of these interacting residues, as reading them directly from the visual representation is challenging. Could you please provide guidance on the specific commands or procedures within Chimera that would allow me to: • Select residues in one molecule that are within 4 Å of the other molecule. • Generate and export a list of these selected residues for further analysis. I have attempted various selection and reporting commands but have not yet achieved the desired outcome. Detailed instructions or references to relevant documentation would be greatly appreciated. Thank you very much for your assistance. Best regards, Rashmi
Also make sure you know which program you are using. I answered for UCSF ChimeraX (not Chimera) because this question was emailed to chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> Elaine
On Feb 27, 2025, at 10:57 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Rashmi, I can't give the specific commands for your project since you didn't give specific information: I don't know if these molecules are in different models, or different chains in the same model, and whether they also contain other chains and/or molecules like water and ligands. So I can only describe things generally.
The general approach is to select the nearby residues and then use the info command to write a list of the selection.
(1) Selecting the residues. There are lots of ways to select the nearby residues, either using the menu/GUIs or commands. The menus/GUIs might be easier if you are a beginner. For the mostly-menu approach, you'd first select one molecule (with Select menu or "select" command), and then use menu: Select... Zone. For the command approach, see "select zone" help and examples therein: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/select.html#zone>
(2) Listing the selection. You can use command
info residues sel
... just to show it in the Log, or to save it to a text file, for example ~/Desktop/residues.txt, use another option:
info residues sel saveFile ~/Desktop/residues.txt
see "info residues" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 27, 2025, at 8:26 AM, Rashmi Aggarwal via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear UCSF Chimera Support Team, I hope this message finds you well. I am currently working on analyzing interactions between two molecular structures using UCSF Chimera. I have successfully identified residues that are within a 4 Å distance between the two molecules. However, I am encountering difficulties in obtaining a clear, textual list of these interacting residues, as reading them directly from the visual representation is challenging. Could you please provide guidance on the specific commands or procedures within Chimera that would allow me to: • Select residues in one molecule that are within 4 Å of the other molecule. • Generate and export a list of these selected residues for further analysis. I have attempted various selection and reporting commands but have not yet achieved the desired outcome. Detailed instructions or references to relevant documentation would be greatly appreciated. Thank you very much for your assistance. Best regards, Rashmi
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participants (2)
-
Elaine Meng -
Rashmi Aggarwal