Re: [Chimera-users] Question about selecting residues
Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia ________________________________ From: Zhang, Bixia <bixia.zhang@wsu.edu> Sent: Friday, September 27, 2019 10:11 To: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: Question about selecting residues Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia ________________________________ From: Zhang, Bixia Sent: Friday, September 27, 2019 10:06 To: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Question about selecting residues Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia
Dear Bixia, The “smart initial display” (what is shown automatically when you open the structure) uses the same rules as the ribbons preset described here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets> "most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.” This is just to show the parts of the structure that might be interesting to many people. However, we are not claiming that they are the only interactions or all interactions. Depending on how you define “interaction,” you can use several different methods described below to select residues around the ligand, and then write a list of those residues with menu: Actions… Write List. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#writespec> Three ways to select residues that might be interacting with the ligand: (1) select residues near your ligand based on distance cutoff, which could be whatever you want (not necessarily 3.6 angstroms). E.g. select your ligand molecule (many ways: with Ctrl-click on atom and then press keyboard up arrow to select whole residue, or menu: Select… Residue…[ligand residue name]) and then use menu: Select… Zone, <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/menu.html#menuselect> ... or use command-line zone specifications, e.g. command: select ligand zr<4.2 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones> (2) select residues with H-bonds to your ligand. See tool “FindHBond” or command “findhbond” … they have an option to select <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html> (3) select residues with contacts to your ligand. See tool “Find Clashes/Contacts” or command “findclash” … they have an option to select <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> You can also take a look at the tutorial “Structure Analysis and Comparison” for examples of using those tools. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 27, 2019, at 10:14 AM, Zhang, Bixia <bixia.zhang@wsu.edu> wrote:
Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia
Thank you Elaine! That's really helpful. I appreciate your help. Have a good weekend! Best, Bixia ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Friday, September 27, 2019 12:16 To: Zhang, Bixia <bixia.zhang@wsu.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Question about selecting residues Dear Bixia, The “smart initial display” (what is shown automatically when you open the structure) uses the same rules as the ribbons preset described here: <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_menu.html-23menupresets&d=DwIFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=q1mYXF6f1yigLpwDDHFxqXhI9hzQP_ClRCBU_ohonVs&m=MaLbhIAHV3UW9TKgdIpSxQiDbIkw57wmOW4jt1ZGNn4&s=rVjmwazdsLzNkzIAmKDN1hKSAaDAAlB-QH9ssnlkMSQ&e= > "most peptide and nucleic acid chains as ribbons, plus atomic detail (excluding hydrogens on carbon atoms) for residues within 3.6 Å of a ligand residue or metal ion. Atomic detail is also used for chains that are very short.” This is just to show the parts of the structure that might be interesting to many people. However, we are not claiming that they are the only interactions or all interactions. Depending on how you define “interaction,” you can use several different methods described below to select residues around the ligand, and then write a list of those residues with menu: Actions… Write List. <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_menu.html-23writespec&d=DwIFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=q1mYXF6f1yigLpwDDHFxqXhI9hzQP_ClRCBU_ohonVs&m=MaLbhIAHV3UW9TKgdIpSxQiDbIkw57wmOW4jt1ZGNn4&s=dbj1q9dEGkclyo6PizbdpLz21_E9cl95ifr7iPErdmg&e= > Three ways to select residues that might be interacting with the ligand: (1) select residues near your ligand based on distance cutoff, which could be whatever you want (not necessarily 3.6 angstroms). E.g. select your ligand molecule (many ways: with Ctrl-click on atom and then press keyboard up arrow to select whole residue, or menu: Select… Residue…[ligand residue name]) and then use menu: Select… Zone, <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_selection.html&d=DwIFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=q1mYXF6f1yigLpwDDHFxqXhI9hzQP_ClRCBU_ohonVs&m=MaLbhIAHV3UW9TKgdIpSxQiDbIkw57wmOW4jt1ZGNn4&s=EZMkwUasz93N26h3Ehg_-vIYsMm-IgK8rakn3cj22ZI&e= > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_menu.html-23menuselect&d=DwIFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=q1mYXF6f1yigLpwDDHFxqXhI9hzQP_ClRCBU_ohonVs&m=MaLbhIAHV3UW9TKgdIpSxQiDbIkw57wmOW4jt1ZGNn4&s=hjDHPEM1ZWhR-dei5rQ-2yZ81EAdofCVN1arJG1UO4Y&e= > ... or use command-line zone specifications, e.g. command: select ligand zr<4.2 <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_atom-5Fspec.html-23zones&d=DwIFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=q1mYXF6f1yigLpwDDHFxqXhI9hzQP_ClRCBU_ohonVs&m=MaLbhIAHV3UW9TKgdIpSxQiDbIkw57wmOW4jt1ZGNn4&s=w2iTCj23EtYFS0UL8OaXWvDM4R1CT_OWpkhapVWR468&e= > (2) select residues with H-bonds to your ligand. See tool “FindHBond” or command “findhbond” … they have an option to select <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_ContributedSoftware_findhbond_findhbond.html&d=DwIFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=q1mYXF6f1yigLpwDDHFxqXhI9hzQP_ClRCBU_ohonVs&m=MaLbhIAHV3UW9TKgdIpSxQiDbIkw57wmOW4jt1ZGNn4&s=7T8k_BAaSljs5TbwoV3lQPx8iJ33N3pL5CzFZ3vxpNM&e= > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_findhbond.html&d=DwIFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=q1mYXF6f1yigLpwDDHFxqXhI9hzQP_ClRCBU_ohonVs&m=MaLbhIAHV3UW9TKgdIpSxQiDbIkw57wmOW4jt1ZGNn4&s=4JpRn2mcjHkGap2LVi6k3Xt5tazWKEJLb5RcJNpO7EI&e= > (3) select residues with contacts to your ligand. See tool “Find Clashes/Contacts” or command “findclash” … they have an option to select <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_ContributedSoftware_findclash_findclash.html&d=DwIFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=q1mYXF6f1yigLpwDDHFxqXhI9hzQP_ClRCBU_ohonVs&m=MaLbhIAHV3UW9TKgdIpSxQiDbIkw57wmOW4jt1ZGNn4&s=rd8lkk50uD9VX0gFIifcEoCt42VbqAuJtO-FGzTeZ14&e= > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_midas_findclash.html&d=DwIFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=q1mYXF6f1yigLpwDDHFxqXhI9hzQP_ClRCBU_ohonVs&m=MaLbhIAHV3UW9TKgdIpSxQiDbIkw57wmOW4jt1ZGNn4&s=HhUrHD9oooKnFS4rYMvj2GprRsXMuDhGDqZaG2R2oss&e= > You can also take a look at the tutorial “Structure Analysis and Comparison” for examples of using those tools. <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chimera_docs_UsersGuide_tutorials_squalene.html&d=DwIFaQ&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=q1mYXF6f1yigLpwDDHFxqXhI9hzQP_ClRCBU_ohonVs&m=MaLbhIAHV3UW9TKgdIpSxQiDbIkw57wmOW4jt1ZGNn4&s=4JT7S2REbs6KiJPUK5cAiYauOTeNSg1Mg-qHx-heOkE&e= > I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 27, 2019, at 10:14 AM, Zhang, Bixia <bixia.zhang@wsu.edu> wrote:
Dear Chimera Developers, I have a question when I use Chimera these days. I was looking for the residues that interact with my ligand. I notice that when I open the pdb, it will show the residues' side chains automatically. I am wondering how you select those residues (by what principle that you decide it is interacting with ligand). And is there a list for the residues? I want to marked out the amino acids on my sequence but it is very hard to count all of them. I hope to get help from you. Thank you very much! Best, Bixia
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Elaine Meng -
Zhang, Bixia