RNA structure restraints

[cornwero]

Hi, this is a nice tool!

In our lab, we do lots of RNA-protein complex structure determination. The H-bond restraints are helpful, but the H-bonds can be satisfied with many different geometries if the electron density is a bit weaker. This leads to many kinked or twisted base pairs

It would be a significant improvement to also support restraints on base-pair planarity, or to 'force' an A-form conformation.
A means to modify the slop distance and slop angle parameters from the chimera gui would be awesome!
Thanks!
-Rob

[tristanic]

Yes, I can see the value in that. Will put it on the to-do list. You can in principle already take the "force an A-form conformation" route: use your favourite tool to generate an idealised version with your sequence, then use that as the template for ISOLDE's reference-model distance restraints.

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On Thu, Aug 20, 2026 at 6:29 PM cornwero ***@***.***> wrote: *cornwero* created an issue (tristanic/isolde#41) <#41> Hi, this is a nice tool! In our lab, we do lots of RNA-protein complex structure determination. The H-bond restraints are helpful, but the H-bonds can be satisfied with many different geometries if the electron density is a bit weaker. This leads to many kinked or twisted base pairs Image: Image (view on web) <https://github.com/user-attachments/assets/825a8b44-6404-4d0b-a2da-ba6fd9292b3f> Image: Image (view on web) <https://github.com/user-attachments/assets/23abed09-8a6e-4bf3-8a61-adb29007bece> It would be a significant improvement to also support restraints on base-pair planarity, or to 'force' an A-form conformation. — Reply to this email directly, view it on GitHub <#41?email_source=notifications&email_token=AFM54YFGICDUVU23T6G5F5D5K4YOHA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NJSGA3DCNJUGE3DHJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFM54YE7DXQTZJUMHCMBH4T5K4YOHAVCNFSNUABFKJSXA33TNF2G64TZHMZDENZWGAYTOMRZHNEXG43VMU5TKMRQGYYTKNBRGYZ2C5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AFM54YCMRNK2LTCX4V247TT5K4YOHA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NJSGA3DCNJUGE3DHJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2KUZTPN52GK4S7NFXXG> and Android <https://github.com/notifications/mobile/android/AFM54YCG2FAIZWOPIU3Z4CL5K4YOHA5CNFSL4Z3JMQ5C6L3HNF2C22DVMIXUS43TOVSS6NJSGA3DCNJUGE3DHJTSMVQXG33OVJZXKYTTMNZGSYTFMSSWK5TFNZ2K4ZTPN52GK4S7MFXGI4TPNFSA>. Download it today! You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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[gghanim]

The ability to enforce planarity restraints (base-base or side chain-base) would be so helpful to many of us!
It would also be so helpful to have the ability to enforce RNA rotamers or sugar pucker in the way that rotamers are handled for side chains. RNA backbone is rotameric, Murray et al., 2003.
We love using Isolde and have always wished for more features for building RNA and DNA.

[cornwero]

if you are down to work on this, I also noticed that in weaker electron density regions, multiple sugar puckers satisfy electron density, so it would be great to be able to restrain the sugar pucker to C3' or C2'.