[Chimera-users] How to insert a nucleotide to a pdb

[Magdalena Riad]

Hi Elaine,

Thanks a lot for your answer.

I actually want to insert the nucleotides into the middle of an RNA sequence. Then that gets even trickier I guess?

Cheers,
Magdalena

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________________________________
Från: Elaine Meng <meng at cgl.ucsf.edu>
Skickat: Tuesday, October 25, 2022 7:28:13 PM
Till: Magdalena Riad <magdalena.riad at ki.se>
Kopia: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Ämne: Re: [Chimera-users] How to insert a nucleotide to a pdb

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Hi Magdalena,
Sorry, there is no command to add a nucleotide residue on the end of a nucleotide chain.

You could still try to do this in Chimera, but it may be tricky and have several steps:

(1) find another PDB structure that has those two residues, then open it, delete all the rest of that structure - OR -  use the Start Structure section of the Build Structure tool (in menu under Tools... Structure Editing) to build the dinucleotide.  This will only build helical conformations, however.

(2) use the Join Models section in the Build Structure tool to combine and bond the 2 residues into your original structure.

It may be hard to get the right angles/position, so you may have to rotate some bonds after that (see Adjust Torsions section of the Build Structure tool).

Click the Help button on the Build Structure tool for details, or see the copy of the same information at our website:
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fediting%2Fediting.html&data=05%7C01%7Cmagdalena.riad%40ki.se%7C31d4f661cfdc40b8f0d308dab6ae4f02%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638023157018301548%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=i3FQM%2BQKBpRtum7eZqw8B35f1K2BkuLwbsLMixSmeXA%3D&reserved=0>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 25, 2022, at 4:56 AM, Magdalena Riad via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi,
> I have a pdb-file of the ribosome and would like to insert two nucleotides to one of the rRNA-chains. How do I do that? I’ve found the addaa command for amino acids, is there a similar one for nucleotides?
> Best regards,
> Magdalena




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