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General discussions (Q&As) / zero or negative helical rise?
« on: March 25, 2013, 01:49:52 pm »
Hi, Xiangjun!

I am a little confused about zero or even negative helical rise for some base-pair step parameter output, for example DNA in PDBID 1XVK. Do you have any comment or reference on this ? Thanks a lot!


General discussions (Q&As) / question on +/- signs of local bp parameters
« on: January 11, 2013, 01:35:30 pm »

I am confused with the meaning of the +/- values of the local base pair parameters, like opening, shear, ect. I noticed in a Bform DNA duplex, a AT(looking from the primary strand) pair usually have a + opening while a TA pair usually has a -opening angles. Is +/- supposed to differentiate this kind of situation? I checked the two pair in pymol and can not tell any differences between the opening the + and - opening angles(both open to the major groove side.) Thanks!

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.