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 ________________________________ To unsubscribe from the COOT list, click the following link: Bad URL Removed - see why - https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=COOT&A=1 CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/