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

[Elaine Meng]

Hi Magdalena,
Chimera does not include tools to insert nucleotides in the middle of a chain.  

However, take a look at the RNArtist program for RNA modeling -- it has a lot of fancy features and interfaces with Chimera (or ChimeraX) for the display:
<https://github.com/fjossinet/RNArtist>

There is also the program Assemble2 by the same author, also works with Chimera:
<https://www.rbvi.ucsf.edu/chimera/plugins/plugins.html#assemble2>
<http://bioinformatics.org/assemble/index.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 Oct 25, 2022, at 11:03 PM, Magdalena Riad via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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 
> 
> Skickat från Outlook för iOS
> 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
>  
> [Du får inte e-post ofta från meng at cgl.ucsf.edu. Läs om varför det här är viktigt påhttps://aka.ms/LearnAboutSenderIdentification ]
> 
> 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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