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Questions and answers => General discussions (Q&As) => Topic started by: feix on July 23, 2008, 10:54:49 am

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Title: calculate step parameters of a funny step
Post by: feix on July 23, 2008, 10:54:49 am

HI! Xiangjun:
I can't get the values of step parameters of step 57 in the pdb file attached here (2f8n.pdb). I checked the 3D-structure. The base pair 58 (58 G and 233 C) in dimer step 57 is a funny base pair, whose Propeller is -60 degree ( I attach a picture of step 57). I guess, 3DNA might put some constrains to base pairs so that I can't get the value of step parameters of step 57. How can I avoid the constrains and get the values of the step parameters

Thanks!

Best,

Fei

Title: Re: calculate step parameters of a funny step
Post by: xiangjun on July 23, 2008, 10:34:44 pm

Read the FAQ #6. Specifically, check file 'misc_3dna.par': one of the geometric constraints is the angle between base normals, with a default of 65 degrees. The base pair 58 (58 G and 233 C) you referred to could be larger than it.

As suggested in previous forum posts, you can always manually edit the 'find_pair' output before feeding it into 'analyze' to get the parameters of arbitrary bps or steps you are interested in.

HTH,

Xiang-Jun

Title: Re: calculate step parameters of a funny step
Post by: feix on July 24, 2008, 12:35:12 pm

Hi! Xiangjun:
Thanks! I changed the setting of misc_3dna.par so that 3dna does not recognize the step 57 as a breakage of helices. Everything works fine now.

Best,

Fei

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University