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<div>Hi Elaine,</div>
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<div dir="ltr">Thanks a lot for your answer. </div>
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<div dir="ltr">I actually want to insert the nucleotides into the middle of an RNA sequence. Then that gets even trickier I guess?</div>
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<div dir="ltr">Cheers,</div>
<div dir="ltr">Magdalena </div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Från:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Skickat:</b> Tuesday, October 25, 2022 7:28:13 PM<br>
<b>Till:</b> Magdalena Riad <magdalena.riad@ki.se><br>
<b>Kopia:</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Ämne:</b> Re: [Chimera-users] How to insert a nucleotide to a pdb</font>
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<div class="PlainText">[Du får inte e-post ofta från meng@cgl.ucsf.edu. Läs om varför det här är viktigt på
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Hi Magdalena,<br>
Sorry, there is no command to add a nucleotide residue on the end of a nucleotide chain.<br>
<br>
You could still try to do this in Chimera, but it may be tricky and have several steps:<br>
<br>
(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.<br>
<br>
(2) use the Join Models section in the Build Structure tool to combine and bond the 2 residues into your original structure.<br>
<br>
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).<br>
<br>
Click the Help button on the Build Structure tool for details, or see the copy of the same information at our website:<br>
<<a href="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</a>><br>
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I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Oct 25, 2022, at 4:56 AM, Magdalena Riad via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:<br>
><br>
> Hi,<br>
> 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?<br>
> Best regards,<br>
> Magdalena<br>
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