Hello! I am using the Build structure to create DNA duplexes with ATGC bases. However, I want to insert Ts that are slightly modified. I can go in and modify each T but I was wondering if I can make a modified-T “template” , assign it a new letter (say X) and then use it in the Build structure function. The backbone and base pairing rules of the new T would be the same. For example, I want to create a T that has an amino linker… Regards, Divita
Hi Divita, While theoretically possible via some precise and difficult tinkering with data files in BuildStructure as well as it's placeNucleotide() routine, I wouldn't recommend that approach -- it's just too hard and too much work. What I would recommend instead is to add your modified Ts as regular Ts and afterward select the atoms where the modification occurs and use a custom Python script to make the modification. The script would loop through chimera.selection.currentAtoms() and use chimera.molEdit.addDihedralAtom(new_atom_name, element, from_atom, dihed2_atom, dihed3_atom, bond_dist, angle, dihedral, bonded=True) to add the modification atom by atom. Let me know if you need more guidance than this. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 8, 2021, at 11:41 AM, Divita Mathur <dmathur4@gmu.edu> wrote:
Hello!
I am using the Build structure to create DNA duplexes with ATGC bases. However, I want to insert Ts that are slightly modified. I can go in and modify each T but I was wondering if I can make a modified-T “template” , assign it a new letter (say X) and then use it in the Build structure function. The backbone and base pairing rules of the new T would be the same.
For example, I want to create a T that has an amino linker…
Regards, Divita _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev>
Hi Eric I see, not a problem. Instead of script I have used the Modify structure and change one hydrogen at a time to add the next atom by selecting the correct number of bonds and shape (linear/trigonal/tetrahedral). Is that another acceptable way of doing it? Have you considered adding other nucleic acids in the alphabet available in Chimera? Such as PNA or LNA? I have built them from scratch and then used “Minimize Structure” for achieving the reasonable bond angle/lengths. Thanks, Divita From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Friday, January 8, 2021 at 4:49 PM To: Divita Mathur <dmathur4@gmu.edu> Cc: chimera-dev@cgl.ucsf.edu <chimera-dev@cgl.ucsf.edu> Subject: Re: [chimera-dev] Building custom nucleotides Hi Divita, While theoretically possible via some precise and difficult tinkering with data files in BuildStructure as well as it's placeNucleotide() routine, I wouldn't recommend that approach -- it's just too hard and too much work. What I would recommend instead is to add your modified Ts as regular Ts and afterward select the atoms where the modification occurs and use a custom Python script to make the modification. The script would loop through chimera.selection.currentAtoms() and use chimera.molEdit.addDihedralAtom(new_atom_name, element, from_atom, dihed2_atom, dihed3_atom, bond_dist, angle, dihedral, bonded=True) to add the modification atom by atom. Let me know if you need more guidance than this. --Eric Eric Pettersen UCSF Computer Graphics Lab On Jan 8, 2021, at 11:41 AM, Divita Mathur <dmathur4@gmu.edu<mailto:dmathur4@gmu.edu>> wrote: Hello! I am using the Build structure to create DNA duplexes with ATGC bases. However, I want to insert Ts that are slightly modified. I can go in and modify each T but I was wondering if I can make a modified-T “template” , assign it a new letter (say X) and then use it in the Build structure function. The backbone and base pairing rules of the new T would be the same. For example, I want to create a T that has an amino linker… Regards, Divita _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu<mailto:Chimera-dev@cgl.ucsf.edu> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev<https://secure-web.cisco.com/1ykp3YKsJq0cfXwKZWSDsOvjauIwh6vV7gPmDePEbSLvfRztIFIV7qLEHxmUbLv6Wuh4NQpMEo1J83zgtd6tgrcHMKIAkteIfBkpTUsyf_ngULdtRuJPMG9TQ_1eaXJFifqFa7EvkGvp_tmnCW2aF2EMnVw6SZH7bOgWe2zLRw-N6qxkyoUhqwDbWK_VCzhvzc8NYie35y_gSm4CfxEVtcDXYxRFS50-pdR971YR8laRq7unKcMGya8ZZMu8KJ0psjR43nOSV23H8ARo6h2gQAcAKLwtWCWkt7_F9V6Ecx682xq-2N31O1cKmm7fhInCLs49qBN2fLfpoPoDn540YApe_Vai11MwhR55VMx9CP5ORie8kiRLwlvTZUUEDOSmmc1WVKsJQkb_QzWiv4kb68QpaoYYngWaLawV56ZW0PW-4Mf18gjeUcVZRMBPU7VQt/https%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-dev>
Hi Divita, A few answers between your questions below.
On Jan 8, 2021, at 4:10 PM, Divita Mathur <dmathur4@gmu.edu> wrote:
Hi Eric
I see, not a problem. Instead of script I have used the Modify structure and change one hydrogen at a time to add the next atom by selecting the correct number of bonds and shape (linear/trigonal/tetrahedral). Is that another acceptable way of doing it?
That is the only way, if you are using Chimera. Eric was suggesting a way to do exactly the same Chimera functions with code instead, since you asked on the programming mailing list (chimera-dev), but the method is the same. For future reference, if you just want to ask non-programming questions about Chimera, the better e-mail address is chimera-users@cgl.ucsf.edu
Have you considered adding other nucleic acids in the alphabet available in Chimera? Such as PNA or LNA? I have built them from scratch and then used “Minimize Structure” for achieving the reasonable bond angle/lengths.
No, we have not been planning to add other nucleotides, especially not any with different backbones like PNA (peptide nucleic acids) and LNA (locked nucleic acids).
Thanks, Divita
Best, Elaine ---- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Friday, January 8, 2021 at 4:49 PM To: Divita Mathur <dmathur4@gmu.edu> Cc: chimera-dev@cgl.ucsf.edu <chimera-dev@cgl.ucsf.edu> Subject: Re: [chimera-dev] Building custom nucleotides
Hi Divita, While theoretically possible via some precise and difficult tinkering with data files in BuildStructure as well as it's placeNucleotide() routine, I wouldn't recommend that approach -- it's just too hard and too much work. What I would recommend instead is to add your modified Ts as regular Ts and afterward select the atoms where the modification occurs and use a custom Python script to make the modification. The script would loop through chimera.selection.currentAtoms() and use chimera.molEdit.addDihedralAtom(new_atom_name, element, from_atom, dihed2_atom, dihed3_atom, bond_dist, angle, dihedral, bonded=True) to add the modification atom by atom. Let me know if you need more guidance than this.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 8, 2021, at 11:41 AM, Divita Mathur <dmathur4@gmu.edu> wrote:
Hello!
I am using the Build structure to create DNA duplexes with ATGC bases. However, I want to insert Ts that are slightly modified. I can go in and modify each T but I was wondering if I can make a modified-T “template” , assign it a new letter (say X) and then use it in the Build structure function. The backbone and base pairing rules of the new T would be the same.
For example, I want to create a T that has an amino linker…
Regards, Divita
Thank you! I’ll keep in mind the other email address. Regards, Divita From: Elaine Meng <meng@cgl.ucsf.edu> Date: Saturday, January 9, 2021 at 11:26 AM To: Divita Mathur <dmathur4@gmu.edu> Cc: Chimera Dev <chimera-dev@cgl.ucsf.edu> Subject: Re: [chimera-dev] Building custom nucleotides Hi Divita, A few answers between your questions below.
On Jan 8, 2021, at 4:10 PM, Divita Mathur <dmathur4@gmu.edu> wrote:
Hi Eric
I see, not a problem. Instead of script I have used the Modify structure and change one hydrogen at a time to add the next atom by selecting the correct number of bonds and shape (linear/trigonal/tetrahedral). Is that another acceptable way of doing it?
That is the only way, if you are using Chimera. Eric was suggesting a way to do exactly the same Chimera functions with code instead, since you asked on the programming mailing list (chimera-dev), but the method is the same. For future reference, if you just want to ask non-programming questions about Chimera, the better e-mail address is chimera-users@cgl.ucsf.edu
Have you considered adding other nucleic acids in the alphabet available in Chimera? Such as PNA or LNA? I have built them from scratch and then used “Minimize Structure” for achieving the reasonable bond angle/lengths.
No, we have not been planning to add other nucleotides, especially not any with different backbones like PNA (peptide nucleic acids) and LNA (locked nucleic acids).
Thanks, Divita
Best, Elaine ---- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Friday, January 8, 2021 at 4:49 PM To: Divita Mathur <dmathur4@gmu.edu> Cc: chimera-dev@cgl.ucsf.edu <chimera-dev@cgl.ucsf.edu> Subject: Re: [chimera-dev] Building custom nucleotides
Hi Divita, While theoretically possible via some precise and difficult tinkering with data files in BuildStructure as well as it's placeNucleotide() routine, I wouldn't recommend that approach -- it's just too hard and too much work. What I would recommend instead is to add your modified Ts as regular Ts and afterward select the atoms where the modification occurs and use a custom Python script to make the modification. The script would loop through chimera.selection.currentAtoms() and use chimera.molEdit.addDihedralAtom(new_atom_name, element, from_atom, dihed2_atom, dihed3_atom, bond_dist, angle, dihedral, bonded=True) to add the modification atom by atom. Let me know if you need more guidance than this.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 8, 2021, at 11:41 AM, Divita Mathur <dmathur4@gmu.edu> wrote:
Hello!
I am using the Build structure to create DNA duplexes with ATGC bases. However, I want to insert Ts that are slightly modified. I can go in and modify each T but I was wondering if I can make a modified-T “template” , assign it a new letter (say X) and then use it in the Build structure function. The backbone and base pairing rules of the new T would be the same.
For example, I want to create a T that has an amino linker…
Regards, Divita
participants (3)
-
Divita Mathur -
Elaine Meng -
Eric Pettersen