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Author Topic: Request for comments on DSSR output before v1.0 release  (Read 4774 times)

Offline xiangjun

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Request for comments on DSSR output before v1.0 release
« 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

Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Offline febos

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Re: Request for comments on DSSR output before v1.0 release
« Reply #1 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:
Code: [Select]
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.
« Last Edit: January 14, 2014, 05:14:28 am by febos »

Offline xiangjun

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Re: Request for comments on DSSR output before v1.0 release
« Reply #2 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
« Last Edit: January 14, 2014, 11:26:14 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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* Original Poster, please provide a summary
* DSSR 2.0 has superseded the 3DNA v2.4 suite

 

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.