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1
General discussions (Q&As) / Re: Circular DNA and Groove Information
« Last post by ry54451 on March 19, 2019, 10:34:39 am »
That sounds great!
It's been my experience that there doesn't need to be a new way of arranging the base pair nor the base pair step parameters except that the first base pair will need to be repeated at the end (N base pairs so N base pair steps) in order to collect the last base pair step data.
2
General discussions (Q&As) / Re: Circular DNA and Groove Information
« Last post by xiangjun on March 18, 2019, 12:15:35 pm »
In addition to groove dimensions for circular DNA or RNA, as you asked in your starting post, do you have any preference on how to list the base-pair step parameters? I am planning to add a new option, tentatively named '--circular', to the 3DNA analyze program. Does it sound good?

Best regards,

Xiang-Jun
3
RNA structures (DSSR) / Re: Using dssr to analyze PDB containing multiple frames
« Last post by xiangjun on March 08, 2019, 10:45:24 pm »
OK. Now I understand your point.

For the analysis of an NMR ensemble or MD trajectories, the --json option is the approach to go. Using 2n2d as an example, as given from DSSR -h or --help, you could:

Code: Bash
  1. x3dna-dssr -i=2n2d.pdb --nmr --json -o=2n2d-dssr.json
  2. # the following command extracts parameters related to the first nucleotide of the first model (with index 0)
  3. jq .models[0].parameters.nts[0] 2n2d-dssr.json

See the thread "DSSR: Analyzing NMR structures - overwritten output files". The R script by Markus should be of help.

Best regards,

Xiang-Jun
4
RNA structures (DSSR) / Re: Using dssr to analyze PDB containing multiple frames
« Last post by jimamoto on March 08, 2019, 10:31:55 pm »
Attached is a few output files that I received when I ran the command.

The exact command entered
x3dna-dssr --input=../../Linear2b_Layer8_24.8-31.0Kcal_noWat_Frame_1-100.pdb --nmr  -o=Lin2_Lay8_NoWat_Frame_1-100-model.out
The output contains only 1 model out of the 100 that were in the pdb.

Also I forgot to mention I am running  v1.7.7-2018apr20 of dssr.

Thank you.
Jason Imamoto
5
RNA structures (DSSR) / Re: Using dssr to analyze PDB containing multiple frames
« Last post by xiangjun on March 08, 2019, 10:16:30 pm »
Please provide an example file, command options, and the output file, to show the problem concretely.

Thanks,

Xiang-Jun
6
RNA structures (DSSR) / Using dssr to analyze PDB containing multiple frames
« Last post by jimamoto on March 08, 2019, 10:14:38 pm »
Hello,
I am trying to use dssr to analyze a pdf file containing multiple frames.  Unfortunately, when I use dssr whether I use --nmr or --json it only gives me information on a single frame.  I have tried adding model to the name of the output file, but it does not produce torsions for each one.  I am new at using dssr and I figure I am making a simple mistake. 
Below are two of the ways I have tried to call dssr.
x3dna-dssr --input=../../Linear2b_Layer8_24.8-31.0Kcal_noWat_Frame_1-100.pdb --nmr -json -o=Lin2_Lay8_NoWat_Frame_1-100-all.json
x3dna-dssr --input=../../Linear2b_Layer8_24.8-31.0Kcal_noWat_Frame_1-100.pdb --nmr  -o=Lin2_Lay8_NoWat_Frame_1-100-model.out

Thank you for your time and help.

Jason Imamoto
7
General discussions (Q&As) / Re: Circular DNA and Groove Information
« Last post by xiangjun on March 08, 2019, 05:05:18 pm »
Hi,

Thanks a lot for your kind words about 3DNA!

Yes, I'd like to incorporate the analysis of circular DNA or RNA into 3DNA. Your attached example looks beautiful and serves as a good starting point. Timewise, I'm recently busy with a deadline, but would hopefully get back to the topic late next week. I'll have a follow-up along this thread once I've something concrete to share.

Best regards,

Xiang-Jun
8
General discussions (Q&As) / Circular DNA and Groove Information
« Last post by ry54451 on March 08, 2019, 03:20:45 pm »
Thanks for an absolutely fantastic software package. I've been able to devote more time to understanding it while improving my own programming skills and you've done a brilliant job with 3DNA.

I wanted to know if you had any plans on incorporating circular analysis? I ask as I work with 336bp and 1014bp circles and would like to get minor-/major-groove data. However, the first and last few entries lack values. I've been looking at the cited paper to get a better idea with maybe calculating it on my own, but I wanted to know if circular analysis was on the radar.

Again, thanks for your time.

Note: I've posted a simple planar circle as an example.
9
RNA structures (DSSR) / Re: Junction definition
« Last post by lijun on March 07, 2019, 02:23:01 pm »
--nested option works!
Thanks,
Jun Li

OK. I got it. I'll look into the issue.

Regarding the definition of (junction) loops, the DSSR paper says:

Quote
In DSSR, a loop forms a ‘closed’ circle with any two sequential nucleotides connected either by a phosphodiester linkage or a canonical base pair, and is specified by the lengths of consecutive bridging-nucleotide segments (Figures 1F and 2C).

The situation becomes less intuitive/obvious when pseudoknots are included. You could try the --nested option to removed pseudoknots to see if the results make more sense.

Best regards,

Xiang-Jun
10
RNA structures (DSSR) / Re: Junction definition
« Last post by xiangjun on March 07, 2019, 11:20:56 am »
OK. I got it. I'll look into the issue.

Regarding the definition of (junction) loops, the DSSR paper says:

Quote
In DSSR, a loop forms a ‘closed’ circle with any two sequential nucleotides connected either by a phosphodiester linkage or a canonical base pair, and is specified by the lengths of consecutive bridging-nucleotide segments (Figures 1F and 2C).

The situation becomes less intuitive/obvious when pseudoknots are included. You could try the --nested option to removed pseudoknots to see if the results make more sense.

Best regards,

Xiang-Jun
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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.