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Author Topic: x3dna_ensemble is not working for hairpin loop structures  (Read 6300 times)

Offline sudhjnu

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x3dna_ensemble is not working for hairpin loop structures
« on: February 10, 2016, 11:10:19 am »
x3dna_ensemble is not working for hairpin loop structures made up of only one strand as for pdb id '2n4l' which contains multiple models. When this file is being processed by x3dna_ensemble, it is prompting the message :
> x3dna_ensemble analyze -e 2n4l.pdb -b bp_order.dat
Process model #1        1 / 10
Not a duplex: <>

I tried this for other loop structures too. Please check this. If i am doing something wrong kindly inform me.

Best,

Sudhanshu Shanker

Offline xiangjun

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Re: x3dna_ensemble is not working for hairpin loop structures
« Reply #1 on: February 10, 2016, 11:55:55 am »
Could you attach your 'bp_order.dat' file?

When analysing multiple models with 'x3dna_ensemble', it helps to try only one structure (with 'find_pair/analyze') to ensure 3DNA is working as expected. You may also want to play with the examples that come with 'x3dna_ensemble analyze -h'.

Did you know "do_x3dna"? You may find it more user-friendly than 'x3dna_ensemble'.

Xiang-Jun

Offline sudhjnu

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Re: x3dna_ensemble is not working for hairpin loop structures
« Reply #2 on: February 11, 2016, 06:50:24 am »
Thank you Xiang-Jun. I checked and found that bp_order.dat file was not correct. Now it is working fine.
Thank you

Sudhanshu Shanker

 

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.