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Author Topic: error bars in DNA parameters  (Read 6991 times)

Offline cllawson

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error bars in DNA parameters
« on: December 17, 2008, 11:11:27 am »
Dear Xiang-Jun,

 Can you advise the best way to determine or estimate error in parameters such as slide, twist, roll, x-displacement for a given estimated coordinate error?   (in our case refinement programs indicate the coordinate error is ~0.3 Angstroms).

thanks,

Cathy

Offline xiangjun

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Re: error bars in DNA parameters
« Reply #1 on: December 17, 2008, 09:56:23 pm »
Hi Cathy,

Quote from: "Cathy"
Can you advise the best way to determine or estimate error in parameters such as slide, twist, roll, x-displacement for a given estimated coordinate error? (in our case refinement programs indicate the coordinate error is ~0.3 Angstroms).

All the nucleic acid analysis programs I know of, 3DNA included, calculates a set of structure parameters (slide, roll etc) based on given x-, y- and z-coordinates in PDB format and the coordinate uncertainty (B-factor) is not taken into account.

In NMR derived structures, one has an ensemble of models that fit the constraints, and analyzing all of them would give a mean/std of the structural parameters. It seems there is only one model in x-ray determined structures, and I do not know how the coordinate error in x-ray crystal structures can be directly applied to estimate errors in parameters. I would imagine that the errors in structure parameters should be relatively insensitive to coordinate error: the parameters are based on base-pair plane(s), averaged over all the base atoms whose uncertainty could conceal out.

Hope this helps a little bit: sorry for not being able to provide a more direct answer. Wilma could provide you with more insights into this issue.

Xiang-Jun

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.