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Questions and answers => RNA structures (DSSR) => Topic started by: xiangjun on January 10, 2014, 03:40:26 pm

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Title: Request for comments on DSSR output before v1.0 release
Post by: xiangjun on January 10, 2014, 03:40:26 pm

Greetings, DSSR users!

It is over ten months since DSSR beta-r01-on-20130303 was first made public. Over the time, thanks to the feedback of many enthusiastic users, DSSR has been continuously developed and improved. I believe the software is now solid enough for v1.0, to be released in the near future.

If you have any comments on DSSR in general, its output style in particular, please do let me know. I will try to accommodate as much of your feedback as practical in the DSSR v1.0 release.

Best regards,

Xiang-Jun

Title: Re: Request for comments on DSSR output before v1.0 release
Post by: febos on January 14, 2014, 05:09:47 am

Hi Dr. Lu.

I want to report a little issue:

when I run dssr on 1FFK i see following info:

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Processing file '1FFK.pdb1' [1FFK]

total number of base pairs: 1406
total number of multiplets: 219
total number of helices: 104
total number of stems: 175
total number of hairpin loops: 66
total number of bulges: 34
total number of internal loops: 63
total number of junctions: 31
total number of non-pairing interactions: 2288
total number of non-loop single-stranded segments: 47
total number of kissing loops: 1
total number of A-minor (type I and II) motifs: 93
total number of ribose zippers: 41 (237)
total number of kink turns: 6
total number of phosphate interactions: 641

Here I don't see number of U-turns however there are 28 U-turns in this pdb-file.

I used commands:

Code: [Select]

x3dna-dssr -i=1FFK.pdb1 -o=1FFK.out1 -note -more -non-pair -u-turn -po4 -break-symbol -long-idstr and

Code: [Select]

x3dna-dssr -i=1FFK.pdb1 -o=1FFK.out1 -u-turn,results are identical.

p/s/ out-file is ok, issue are only in command-line output.

Best regards,
Eugene.

Title: Re: Request for comments on DSSR output before v1.0 release
Post by: xiangjun on January 14, 2014, 11:22:36 am

Hi Eugene,

Thanks for reporting DSSR's omission to report the "total number of U-turns:" in the diagnostic command-line output. This inconsistency has been fixed in DSSR beta-r30, which contains many other significant formatting improvements, and further refinements on loop finding. See below for running DSSR on 1ffk (x3dna-dssr -i=1ffk.pdb -o=1ffk.out -u-turn):

Code: [Select]

Processing file '1ffk.pdb' [1ffk]

total number of base pairs: 1406
total number of multiplets: 219
total number of helices: 104
total number of stems: 175
total number of hairpin loops: 66
total number of bulges: 35
total number of internal loops: 66
total number of junctions: 33
total number of pseudo-knots: 22
total number of non-loop single-stranded segments: 32
total number of kissing loops: 1
total number of A-minor (type I and II) motifs: 93
total number of U-turns: 28
total number of ribose zippers: 41 (237)
total number of kink turns: 6
I will release DSSR beta-r30, presumably the last beta version, in a couple of days. In the meantime, please keep reporting back any other suggestions you may have.

Best regards,

Xiang-Jun

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University