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Questions and answers => General discussions (Q&As) => Topic started by: shuxiang on October 29, 2018, 03:57:11 pm

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Title: How to calculate two reference frames for each base in a base pair
Post by: shuxiang on October 29, 2018, 03:57:11 pm
Hi Xiang-Jun,

I encounter a question when plotting separate frames for each base in a base pair. See the attached picture, each base has its own reference frame.
(http://)

From the ref_frames.dat file, I get the information like following.  If I understand correctly, it looks like the reference frames here are the averaged frames for a base pair.
...     6 A-T   # A:...6_:[.DA]A - B:..19_:[.DT]T
   14.8825    20.6882    10.2718  # origin
    0.9873    -0.1230    -0.1006  # x-axis
   -0.0859    -0.9457     0.3135  # y-axis
   -0.1337    -0.3009    -0.9442  # z-axis

I want to obtain the reference frame for each base in a paired bases. Thank you.

Best,
Shuxiang
Title: Re: How to calculate two reference frames for each base in a base pair
Post by: xiangjun on October 29, 2018, 04:49:00 pm
Hi Shuxiang,

Try to run find_pair with the -s option. For example, with PDB id 355d, you'd get the following:

find_pair -s 355d.pdb
# check file: ref_frames.dat
   24 bases
...     1 C   # A:...1_:[.DC]C
   16.9789    25.9058    25.8821  # origin
   -0.9926     0.0784    -0.0923  # x-axis
    0.1143     0.8582    -0.5004  # y-axis
    0.0400    -0.5073    -0.8609  # z-axis
...     2 G   # A:...2_:[.DG]G
   16.5327    24.5857    22.7653  # origin
   -0.7750     0.6089    -0.1693  # x-axis
    0.6082     0.6457    -0.4617  # y-axis
   -0.1718    -0.4607    -0.8707  # z-axis
......


You could also easily get the base reference frame using DSSR with the --json option. For example,

x3dna-dssr -i=355d.pdb --json | jq -c .nts[0].frame
# you'd get the following for A.DC1
{"rmsd":0.01,"origin":[16.979,25.906,25.882],"x_axis":[-0.993,0.078,-0.092],
"y_axis":[0.114,0.858,-0.5],"z_axis":[0.04,-0.507,-0.861],"quaternion":[0.034,0.05,0.963,-0.262]}


HTH,

Xiang-Jun
Title: Re: How to calculate two reference frames for each base in a base pair
Post by: shuxiang on October 29, 2018, 04:59:25 pm
Both methods work. Thank you so much. :)

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