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Questions and answers > General discussions (Q&As)
How to calculate two reference frames for each base in a base pair
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shuxiang:
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.
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
xiangjun:
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
shuxiang:
Both methods work. Thank you so much. :)
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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.