Thanks Christian, I might try editing the PDB but it's looking like Replace 
Residue, as Paul suggested, could keep me from inadvertently making chemistry 
errors.
________________________________
From: Biertuempfel, Christian (NIH/NHLBI) [E] <christian.biertuemp...@nih.gov>
Sent: Tuesday, March 25, 2025 12:09 PM
To: Dan Richman <d.e.rich...@jhu.edu>; COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK>
Subject: Re: Changing RNA types to DNA


      External Email - Use Caution



Hi Dan,

What about a text editor? My favorite is nedit for such things as you can 
select vertically (Ctrl + click or Ctrl + Shift + click) and replace only 
selection (optionally with regular expression).



Cheers,

christian





From: Mailing list for users of COOT Crystallographic Software 
<COOT@JISCMAIL.AC.UK> on behalf of Dan Richman 
<000096f8a22c9ed9-dmarc-requ...@jiscmail.ac.uk>
Date: Tuesday, March 25, 2025 at 12:01
To: COOT@JISCMAIL.AC.UK <COOT@JISCMAIL.AC.UK>
Subject: [EXTERNAL] Changing RNA types to DNA

Hi Coot community,



I've wound up with nucleic acid chains that have a mix of A, C, G, DT, and I'd 
like to change the A, C, G to DA, DC, DG.



But:



Simple Mutate only offers the same A, C, G ribonucleotides, not deoxy types.



Scheme scripting with a command of the form (mutate-nucleotide-range imol 
chain-id resno-start resno-end sequence),

such as

(mutate-nucleotide-range 0 "A" 1 5 DGDCDADTDC)

returns the error that the string length must match the number of residues, so 
I'm not sure how to encode the "deoxy" part of the identifier.



How would you go about changing RNA to DNA?



Thanks!



--

Dan Richman, PhD   (he/him/his)

Research Associate, James Berger Lab

Dept of Biophysics and Biophysical Chemistry

Johns Hopkins University School of Medicine

mobile: 201-669-0967



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