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lorenzo-rovigatti / oxDNA

A new version of the code to simulate the oxDNA/oxRNA models, now equipped with Python bindings
https://dna.physics.ox.ac.uk/
GNU General Public License v3.0
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(OAT Question) Computing Twist between bp #58

Closed thoswope17 closed 1 year ago

thoswope17 commented 1 year ago

Hi,

Sorry if this is misplaced... I work with Daniel Hollis and I believe he's asked questions here before.

We have recently been studying helical pitch/twist angles. I noticed in a build of standalone oat (before the oxDNA + oat merge) that there used to be a function in UTILS/geom.py called get_turn_per_bp that we think might have been used to compute this.

We were wondering if this is applicable at all to oxDNA2 model (we think we found a formula for helicity vector in oxDNA1 model in paper: https://arxiv.org/abs/1009.4480 ). I thought maybe not as this function cruxes on backbone-backbone vector of the two bp, which makes more sense in oxDNA1 model than oxDNA2 model, but maybe I don't yet fully understand it.

Let me know if anything is unclear.

Thanks, Tommy Swope

ErikPoppleton commented 1 year ago

Geom.py originally came from @sulcgroup, perhaps he can share more about its original purpose. Looking at it, I think that function is only applicable to the DNA1 model because it uses the positions of the backbones, which are offset from the helix axis in the DNA2 model. It is also hardcoded to get the twist angle for just a single fully-complimentary duplex, so unless that is exactly your system it would need to be rewritten anyway. You could probably use the same method from that function, but replace the backbone site with the base site (see the get_r function in persistence_length.py for an example of using oxpy to get base sites).

If anybody wants to take a look at the old geom.py, it can be found here

ErikPoppleton commented 1 year ago

That all being said, if you end up re-implementing it, perhaps using the output file from duplex_finder.py to give the average helical twist for a structure, I would be happy to merge it in as a pull request.

supers1x commented 1 year ago

Hi, supporting infomation from this paper may help J. Chem. Phys. 146, 214902 (2017)

thoswope17 commented 1 year ago

Thank you both for the info. The supplement to that paper is very helpful/relevant to us, and I was unaware of it (only the main article). We will let you know if we do end up writing code relevant to this.

ErikPoppleton commented 1 year ago

Great, thanks! I'll go ahead and close this, but feel free to keep responding or open a new issue if you have further questions/issues.