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Author Topic: Stacking parameters  (Read 835 times)

Offline spoblete

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Stacking parameters
« on: December 27, 2018, 01:54:48 pm »
Greetings.

I would like to know more specifically the parameters used in the base-stacking classification. I have seen that some almost-perpendicular pairs of bases are annotated as stacked, so I would like to know if the criteria is based uniquely on the hull overlap or if they belong to a more specific perpendicular stacking interaction set.

Many thanks in advance.

Simón.

Offline xiangjun

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Re: Stacking parameters
« Reply #1 on: December 27, 2018, 02:08:45 pm »
Hi Simón,

Thanks for using DSSR and for posting your questions on the Forum.

You've touched a subtle, technical point. In DSSR, stacking is decided by no-zero overlapping area of (extended) base-rings projected on the mean plane of the two base normals. The two bases may be (nearly) parallel and stack well, or they are offset, and at a big angle. So being 'stacked' are not equal, as reflected by the different overlap areas and the angles. Users can filter the DSSR-derived stacks based on these two parameters.

These are just general comments. If you provide some specific examples, we can discuss in more detail.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.