Regarding Usage of ChimeraX for PDB file creation
Hello, Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. Currently, I am using ChimeraX for one of my research projects. I need to build structures and download the PDB files. I can do that for all L amino acid containing peptides, but I don’t know how to use ChimeraX for D amino acid containing peptides. For example, I have a sequence NWF. Now it is available in this standard L format and also in NdWF format. As ChimeraX is not case sensitive, I don’t know how I should give the command to build the structure with D amino acid containing peptide. Secondly, I have some peptides that have Amidation or NH2 at the C terminus. I don’t know how to add this to my structure. Please let me know how to solve this to issues. That will be really helpful for me. Have a great day. -- Yours sincerely Satirtha Saha He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_medium=referral> sahass@beloit.edu<mailto:sahass@beloit.edu> [Image][cid:image002.png@01D9BB19.9CD8CA10]
Hi Satirtha, ChimeraX cannot directly create D-amino acids, but it is easy to change from L- to D-. Let’s say you want to change residue 2 to D-. Just select the carbon alpha of residue 2 and use the “Invert” section of Build Structure to invert the chirality of the carbon alpha substituents. The equivalent command is “build invert :2@ca”. To amidate the C-terminus, select the OXT connected to the terminus and use the “Modify Structure” section of Build Structure to change the OXT to nitrogen with 3 bonds and planar geometry. Depending on what you intend to do with the modified structure you might also want to use that section to change the name of the amidated residue, or put the admidation in a residue of its own. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 20, 2023, at 12:52 PM, Protya, Satirtha via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. Currently, I am using ChimeraX for one of my research projects. I need to build structures and download the PDB files. I can do that for all L amino acid containing peptides, but I don’t know how to use ChimeraX for D amino acid containing peptides. For example, I have a sequence NWF. Now it is available in this standard L format and also in NdWF format. As ChimeraX is not case sensitive, I don’t know how I should give the command to build the structure with D amino acid containing peptide. Secondly, I have some peptides that have Amidation or NH2 at the C terminus. I don’t know how to add this to my structure.
Please let me know how to solve this to issues. That will be really helpful for me. Have a great day.
-- Yours sincerely Satirtha Saha
He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615 <tel:+16084736615> Schedule an Appointment <https://admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_medium=referral> sahass@beloit.edu <mailto:sahass@beloit.edu> <image001.png><image002.png>
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Hi Eric, Thank you for your reply. It was really helpful. I will try to do so and keep you updated. Have a great day. -Satirtha Saha From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Thursday, July 20, 2023 at 4:39 PM To: Protya, Satirtha <ssprotya@illinois.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Regarding Usage of ChimeraX for PDB file creation Hi Satirtha, ChimeraX cannot directly create D-amino acids, but it is easy to change from L- to D-. Let’s say you want to change residue 2 to D-. Just select the carbon alpha of residue 2 and use the “Invert” section of Build Structure to invert the chirality of the carbon alpha substituents. The equivalent command is “build invert :2@ca”. To amidate the C-terminus, select the OXT connected to the terminus and use the “Modify Structure” section of Build Structure to change the OXT to nitrogen with 3 bonds and planar geometry. Depending on what you intend to do with the modified structure you might also want to use that section to change the name of the amidated residue, or put the admidation in a residue of its own. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jul 20, 2023, at 12:52 PM, Protya, Satirtha via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello, Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. Currently, I am using ChimeraX for one of my research projects. I need to build structures and download the PDB files. I can do that for all L amino acid containing peptides, but I don’t know how to use ChimeraX for D amino acid containing peptides. For example, I have a sequence NWF. Now it is available in this standard L format and also in NdWF format. As ChimeraX is not case sensitive, I don’t know how I should give the command to build the structure with D amino acid containing peptide. Secondly, I have some peptides that have Amidation or NH2 at the C terminus. I don’t know how to add this to my structure. Please let me know how to solve this to issues. That will be really helpful for me. Have a great day. -- Yours sincerely Satirtha Saha He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://urldefense.com/v3/__https:/admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_medium=referral__;!!DZ3fjg!_8Erl7t8iiX5E7-rwOwYs6MDt3AXU0SLFr0biBK8-jvpVK-oltrfJXzIu_40jZiQa7QAJk-2DMGjnSo36Td0$> sahass@beloit.edu<mailto:sahass@beloit.edu> <image001.png><image002.png> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/<https://urldefense.com/v3/__https:/mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/__;!!DZ3fjg!_8Erl7t8iiX5E7-rwOwYs6MDt3AXU0SLFr0biBK8-jvpVK-oltrfJXzIu_40jZiQa7QAJk-2DMGjnd7Qmtxd$>
Hi, I have tried to use the methods. I was successful to do so for small sequence. But for larger sequences is there any particular selection command for selecting OXT? Hope to hear from you soon. Have a great day. * Satirtha From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Thursday, July 20, 2023 at 4:39 PM To: Protya, Satirtha <ssprotya@illinois.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Regarding Usage of ChimeraX for PDB file creation Hi Satirtha, ChimeraX cannot directly create D-amino acids, but it is easy to change from L- to D-. Let’s say you want to change residue 2 to D-. Just select the carbon alpha of residue 2 and use the “Invert” section of Build Structure to invert the chirality of the carbon alpha substituents. The equivalent command is “build invert :2@ca”. To amidate the C-terminus, select the OXT connected to the terminus and use the “Modify Structure” section of Build Structure to change the OXT to nitrogen with 3 bonds and planar geometry. Depending on what you intend to do with the modified structure you might also want to use that section to change the name of the amidated residue, or put the admidation in a residue of its own. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jul 20, 2023, at 12:52 PM, Protya, Satirtha via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello, Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. Currently, I am using ChimeraX for one of my research projects. I need to build structures and download the PDB files. I can do that for all L amino acid containing peptides, but I don’t know how to use ChimeraX for D amino acid containing peptides. For example, I have a sequence NWF. Now it is available in this standard L format and also in NdWF format. As ChimeraX is not case sensitive, I don’t know how I should give the command to build the structure with D amino acid containing peptide. Secondly, I have some peptides that have Amidation or NH2 at the C terminus. I don’t know how to add this to my structure. Please let me know how to solve this to issues. That will be really helpful for me. Have a great day. -- Yours sincerely Satirtha Saha He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://urldefense.com/v3/__https:/admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_medium=referral__;!!DZ3fjg!_8Erl7t8iiX5E7-rwOwYs6MDt3AXU0SLFr0biBK8-jvpVK-oltrfJXzIu_40jZiQa7QAJk-2DMGjnSo36Td0$> sahass@beloit.edu<mailto:sahass@beloit.edu> <image001.png><image002.png> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/<https://urldefense.com/v3/__https:/mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/__;!!DZ3fjg!_8Erl7t8iiX5E7-rwOwYs6MDt3AXU0SLFr0biBK8-jvpVK-oltrfJXzIu_40jZiQa7QAJk-2DMGjnd7Qmtxd$>
Hi, Sorry for the previous email. I was able to find the selection command. Thank you. From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Thursday, July 20, 2023 at 4:39 PM To: Protya, Satirtha <ssprotya@illinois.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Regarding Usage of ChimeraX for PDB file creation Hi Satirtha, ChimeraX cannot directly create D-amino acids, but it is easy to change from L- to D-. Let’s say you want to change residue 2 to D-. Just select the carbon alpha of residue 2 and use the “Invert” section of Build Structure to invert the chirality of the carbon alpha substituents. The equivalent command is “build invert :2@ca”. To amidate the C-terminus, select the OXT connected to the terminus and use the “Modify Structure” section of Build Structure to change the OXT to nitrogen with 3 bonds and planar geometry. Depending on what you intend to do with the modified structure you might also want to use that section to change the name of the amidated residue, or put the admidation in a residue of its own. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jul 20, 2023, at 12:52 PM, Protya, Satirtha via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello, Hope this email finds you well. I am Satirtha Saha, an undergrad research assistant at UIUC. Currently, I am using ChimeraX for one of my research projects. I need to build structures and download the PDB files. I can do that for all L amino acid containing peptides, but I don’t know how to use ChimeraX for D amino acid containing peptides. For example, I have a sequence NWF. Now it is available in this standard L format and also in NdWF format. As ChimeraX is not case sensitive, I don’t know how I should give the command to build the structure with D amino acid containing peptide. Secondly, I have some peptides that have Amidation or NH2 at the C terminus. I don’t know how to add this to my structure. Please let me know how to solve this to issues. That will be really helpful for me. Have a great day. -- Yours sincerely Satirtha Saha He/Him/His Beloit College | Class of 2025 Triple Major | Biochemistry, Cognitive Science and Data Analytics Research Assistant | Sweedler Lab | UIUC Admissions Ambassador | Office of Admissions, Beloit College Funding Board Member | Beloit Student Government (BSG) +1(608) 473-6615<tel:+16084736615> Schedule an Appointment<https://urldefense.com/v3/__https:/admissions.beloit.edu/portal/chat?utm_source=www.beloit.edu&utm_medium=referral__;!!DZ3fjg!_8Erl7t8iiX5E7-rwOwYs6MDt3AXU0SLFr0biBK8-jvpVK-oltrfJXzIu_40jZiQa7QAJk-2DMGjnSo36Td0$> sahass@beloit.edu<mailto:sahass@beloit.edu> <image001.png><image002.png> _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/<https://urldefense.com/v3/__https:/mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/__;!!DZ3fjg!_8Erl7t8iiX5E7-rwOwYs6MDt3AXU0SLFr0biBK8-jvpVK-oltrfJXzIu_40jZiQa7QAJk-2DMGjnd7Qmtxd$>
participants (2)
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Eric Pettersen -
Protya, Satirtha