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Author Topic: create a multiple copy from a building block with DSSR-pro  (Read 1421 times)

Offline amirtaghavi

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create a multiple copy from a building block with DSSR-pro
« on: January 28, 2022, 11:23:34 am »
Hello Dr. Lu,

I am using the DSSR-pro and the work flow you provided to create a multiple copy of a 3bp RNA (attached), I was wondering if it is possible to use the DSSR to create the lost backbone connections.

Thanks,
Amir

x3dna-dssr tasks -i=model.pdb --frame-pair=last -o=model1-ref-last.pdb

x3dna-dssr fiber --seq=GG --rna-ds -o=conn.pdb
x3dna-dssr tasks -i=conn.pdb --frame-pair=first --remove-pair -o=ref-conn.pdb

x3dna-dssr tasks --merge-file='model1-ref-last.pdb ref-conn.pdb' -o=temp1.pdb

x3dna-dssr tasks -i=temp1.pdb --frame-pair=last --remove-pair -o=temp2.pdb
x3dna-dssr tasks -i=model.pdb --frame-pair=first -o=model1-ref-first.pdb

x3dna-dssr tasks --merge-file='temp2.pdb model1-ref-first.pdb' -o=duplicate-model.pdb

Offline xiangjun

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Re: create a multiple copy from a building block with DSSR-pro
« Reply #1 on: January 29, 2022, 12:07:35 pm »
Hi Amir,

Thanks for your support of the DSSR project by purchasing an academic license. As noted in the announcement post "No more grant funding for 3DNA/DSSR", I am committed (now in my 'spare time') to making DSSR a brand that stands for quality and value. I strive to provide paying users the best support they can expect from a software product. The objective is to ensure that the time and effort saved by using DSSR well outweighs the licensing charge, particularly the $1,000 one-time fee for academic users. As an example, did you realize how much time and work you save by getting DSSR up and running vs other software tools you are familiar with?

Now, let's get back to your precise question. I understand what you mean, but the information you supplied is insufficient to demonstrate the problem. Could you provide a minimum example that can reproduce exactly what you want to achieve?

DSSR Pro users, particularly those in the (pharmaceutical) industry, are oftentimes concerned about the data they are willing to share with the public. Thus I've been assisting them via email, phone, WeChat, or Zoom: whatever is convenient and effective. We can keep the topic going on the Forum, or you may wish to go private.

Best regards,

Xiang-Jun
« Last Edit: January 30, 2022, 01:03:30 pm by xiangjun »

 

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.