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51
w3DNA -- web interface to 3DNA / can't open the baselist file error for 2 PDB IDs
« Last post by sowmya on October 19, 2022, 07:54:02 am »
Dear Dr. Xiang,

I was trying to calculate the base pair and base step parameters for PDB IDs - 7E9E and 7E9I by uploading the PDB files to the web interface of 3DNA. I am getting a "can't open the baselist file error" for these 2 IDs. I am yet to come across this error for other PDB IDs - I have calculated for around 20 other PDB IDs (deposited after 2019) in the web interface and they were parsed fine. Requesting your suggestions to resolve this error in the web interface.

With regards,
Sowmya
52
Hi Andrea,

DSSR Pro can do what you want very easily, especially in combination with the --json option. See No more grant funding for 3DNA/DSSR.

Base atoms have always been necessary for the identification of nucleotides in order to calculate base-pair and backbone parameters in 3DNA v2.x, including the command you mentioned: analyze -t=torsions.out. However, since 3DNA v2.x is open source for academic uses, you can modify it to meet your needs.

Best regards,

Xiang-Jun
53
Dear Dr. Xiang-Jun Lu,

I used versions of 3DNA earlier than the 2018 versions some time ago, in those versions it was possible to calculate the torsion angles of the sugar-phosphate backbone of DNA, without taking into account the bases, with the following command:

analyze -t = name.tor name.pdb

However in the new versions, this task is not possible anymore, it is necessary to have the nitrogenous bases or at least   N1, C2 or N9, C4 atoms. 

I was wondering if there is a new instruction or way to do that, because it would shorten my work route considerably. One of my study purposes is the optimized fragments of the Sugar-Phosphate Backbone, in these fragments the nitrogenous bases of the DNA are eliminated and replaced by a hydrogen (position N1 or N9) as shown in file attached .

Thank you very much,

Andrea R.



54
Site announcements / Re: Clarification on DSSR licensing
« Last post by xiangjun on August 11, 2022, 09:24:51 am »
Hi Dr. Baulin,

Quote
is it safe to freely use the old DSSR version for academic use according to the old license?

Yes. Keep in mind that such outdated versions are no longer supported or maintained.

Best regards,

Xiang-Jun
55
Site announcements / Re: Clarification on DSSR licensing
« Last post by febos on August 11, 2022, 07:34:37 am »
Hi Dr. Lu!

About two years ago I downloaded DSSR version 2.0 for academic use and since then I built some work using the tool. Only now have I found out that the newest DSSR versions are not freely available anymore. And now I have a question - is it safe to freely use the old DSSR version for academic use according to the old license?

Thank you!

Best regards,
Eugene Baulin
56
Hi Xiangjun:
     When we use 3DNA to analyze the tertiary structure of RNA, we get the local base pair parameters and simple base pair parameters, and know that different base-pair coordinate frames lead to different results. We would like to know what is the relationship between the two base-pair coordinate frames, but we have not found anything after searching. Could you help us solve this problem?

Zhao
57
Site announcements / Re: Download instructions
« Last post by wdz-victor on March 25, 2022, 01:09:21 am »
Hello everyone, how can I get the old version of the program, or how can the new version 2.4 program run through the pymol script. (No x3dna-dssr.exe found in the new program)
58
General discussions (Q&As) / Rebuild with backbone from single-stranded .par file
« Last post by nicalleb on March 21, 2022, 07:39:35 am »
Dear,

I would like to rebuild a stacked nucleobases structure from a .par file (with the 6  base-step parameters, see in attachment). This .par file was obtained by analyzing a single-stranded GTT stack (PDB file) with the command "find pair". If I rebuild my structure from this .par file with the following command :

rebuild -atomic bp_step.par test_rebuild.pdb

I get a structure without backbone and I need the backbone in subsequent calculations.

With the "Rebuilding" module of the online version of X3DNA, I know it is possible to have a structure with backbone, even starting with a .par file for a single-strand (containing only 6 local base-step parameters)

Is it also possible in command line (with the downloaded version of the software) and if so, how ?


Thank you in advance,

Nicolas Callebaut
59
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
60
RNA structures (DSSR) / create a multiple copy from a building block with DSSR-pro
« Last post by amirtaghavi 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
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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.