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<font face="Times New Roman, Times, serif">Dear all,<br>
is there a way in Chimera or ChimeraX to get the unit-cell box
being drawn in another colour than white?<br>
This forces the background to be dark....<br>
Thanks a lot in advance,<br>
Xavier<br>
</font><br>
<div class="moz-cite-prefix">On 26/10/22 08:03, Magdalena Riad via
Chimera-users wrote:<br>
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<div>Hi Elaine,</div>
<div dir="ltr"><br>
</div>
<div dir="ltr">Thanks a lot for your answer. </div>
<div dir="ltr"><br>
</div>
<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>
<div dir="ltr"><br>
</div>
<div dir="ltr">Cheers,</div>
<div dir="ltr">Magdalena </div>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>Från:</b> Elaine
Meng <a class="moz-txt-link-rfc2396E" href="mailto:meng@cgl.ucsf.edu"><meng@cgl.ucsf.edu></a><br>
<b>Skickat:</b> Tuesday, October 25, 2022 7:28:13 PM<br>
<b>Till:</b> Magdalena Riad <a class="moz-txt-link-rfc2396E" href="mailto:magdalena.riad@ki.se"><magdalena.riad@ki.se></a><br>
<b>Kopia:</b> <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>
<a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.edu"><chimera-users@cgl.ucsf.edu></a><br>
<b>Ämne:</b> Re: [Chimera-users] How to insert a nucleotide to
a pdb</font>
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<br>
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>
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<br>
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 <a class="moz-txt-link-rfc2396E" href="mailto:chimera-users@cgl.ucsf.edu"><chimera-users@cgl.ucsf.edu></a> 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>
<br>
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