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Author Topic: Local strand base parameters even for ssDNA  (Read 2536 times)

Offline iagea

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Local strand base parameters even for ssDNA
« on: February 15, 2017, 08:41:51 am »
Dear all,

I would like to know te displacement of a base related with the previous one even if they are not participating in any base pairing.

I run:

find_pair sample.pdb sample.inp
analyze sample.inp


As a result there is one file called auxiliary.par with information about local strands base step parameters. The problem with that information is that it is just available for base pairing bases and it relates also non-consecutive bases.

I tried to change the input file for analyze in order to pass it like a ssDNA and not just with data about base pairs and the output file auxiliary.par just contains information about reference frames.

My question is: How can I modify the input file to analyze in order to obtain local strands base step parameters for each base even if they belong to a ssDNA?

Thank you,
Isabel

Offline xiangjun

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Re: Local strand base parameters even for ssDNA
« Reply #1 on: February 15, 2017, 02:20:35 pm »
Hi Isabel,

Try "find_pair -s": the -s option stands for single strand. Type find_pair -h for more available options.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline iagea

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Re: Local strand base parameters even for ssDNA
« Reply #2 on: February 16, 2017, 01:41:33 am »
Hi Xiang-Jun,

I tried it. However, the result of analyze auxiliary.par is just the reference frames. No data of local strands base step parameters.

Is it possible that the program is not able to compute those values beyond base pairing?

Isabel.

Offline xiangjun

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Re: Local strand base parameters even for ssDNA
« Reply #3 on: February 16, 2017, 10:42:51 am »
Hi Isabel,

Did you look at the main output file with the -s option? Using 355d as an example,

Code: [Select]
find_pair -s 355d.pdb | analyze
The main output file 355d.outs should contain the requested info. If not, please provide a concrete example to show unambiguously what you want.

HTH,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline iagea

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Re: Local strand base parameters even for ssDNA
« Reply #4 on: February 16, 2017, 12:20:19 pm »
Hi Xian-Jun,

You are completely right, I was obsessed with this auxiliary.par file.

Thank you so much, you have been really helpful!

Regards,
Isabel.

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.