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] <[email protected]>
Sent: Tuesday, March 25, 2025 12:09 PM
To: Dan Richman <[email protected]>; [email protected] <[email protected]>
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
<[email protected]> on behalf of Dan Richman
<[email protected]>
Date: Tuesday, March 25, 2025 at 12:01
To: [email protected] <[email protected]>
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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