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

[F.Xavier Gomis-Rüth]

Dear all,
is there a way in Chimera or ChimeraX to get the unit-cell box being 
drawn in another colour than white?
This forces the background to be dark....
Thanks a lot in advance,
Xavier

On 26/10/22 08:03, Magdalena Riad via Chimera-users 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 <https://aka.ms/o0ukef>
> ------------------------------------------------------------------------
> *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 på https://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 
> <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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