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Author Topic: Further questions about inter-base angle calculations  (Read 393 times)

Offline wangshsh

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Further questions about inter-base angle calculations
« on: February 27, 2017, 01:51:20 am »
In the last question, I want to calculate the inter-base angle of the TS state  of  an addition reaction occurred in a dinucleotide monophosphate.  While it was addressed for the TS state, the inter-base angle can not be obtained for the corresponding product even using the --nt-cutoff=0.9 option.  I want to know how can I calculate the inter-base angle of the product. Thanks very much! The pdb file is given in the attachment.


p.s.  According to my own test calculations, the reasons may be due to the  inter-base angle of the product exceeds the threshhold.
« Last Edit: February 27, 2017, 02:30:33 am by wangshsh »

Offline xiangjun

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Re: Further questions about inter-base angle calculations
« Reply #1 on: February 27, 2017, 08:43:48 am »
As a gereneral way to calculate inter-base angles, you could use the following command. Here, I'm using 1ehz as an example:

Code: [Select]
x3dna-dssr -i=1ehz.pdb --json | jq .nts
x3dna-dssr -i=1ehz.pdb --json | jq -c '.nts[] | { nt_id, "z_axis": .frame.z_axis}'

The nts JSON object contains the reference frame for each identified base. Specifically, pay attention to the z_axis vectors for calculating the inter-base angles of any two bases you are interested in. For your 2.pdb file, the results are as below:

Code: [Select]
x3dna-dssr -i=2.pdb --json | jq -c '.nts[] | { nt_id, "z_axis": .frame.z_axis}'
------
{"nt_id":"A.DG1","z_axis":[0.956,0.284,-0.073]}
{"nt_id":"A.DT2","z_axis":[-0.138,0.571,-0.809]}

Have a try and report back how it goes.

Xiang-Jun
« Last Edit: February 27, 2017, 11:15:50 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline xiangjun

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Re: Further questions about inter-base angle calculations
« Reply #2 on: February 27, 2017, 10:38:39 am »
As a follow-up of my previous responses to your structures 1.pdb and 2.pdb, I became curious why  1.pdb has such a huge "distortion" that requires --nt-cutoff=0.9 to be set while 2.pdb does not. The largest I've ever experienced previously was around --nt-cutoff=0.6 from MD simulations.

It turns out that, in 1.pdb, you've wrongly labeled atoms C6 and C7 for A.DT2. Please see the attached figure which compares 1.pdb and 2.pdb. Once C6 and C7 labeling is corrected in 1.pdb, the default setting (--nt-cutoff=0.28) is sufficient for the identification of A.DT2 as a nucleotide, as expected. As mentioned in the DSSR NAR2015 paper, the default setting is based on extensive tests of real-world structures as in the PDB, and it covers even the two dihydrouridines in tRNA (e.g., 1ehz). Any outliers from the default deserve further close attentions, and your case serves as an excellent example.

HTH,

Xiang-Jun
« Last Edit: February 27, 2017, 11:01:23 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.