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Offline lvelve0901

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strange exception
« on: June 30, 2019, 08:48:31 pm »
Hi Xiangjun,

I was trying to use DSSR to parse this attached PDB file.

x3dna-dssr -i=S_000300_115.pdb

However, the program complain an error:

Command: x3dna-dssr -i=S_000300_115.pdb
Date and time: Sun Jun 30 20:57:27 2019
File name: S_000300_115.pdb
    no. of DNA/RNA chains: 1 [_=25]
    no. of nucleotides:    25
    no. of atoms:          796
    no. of waters:         0
    no. of metals:         0
    total number of base pairs: 11
    total number of multiplets: 1
    total number of helices: 2
    total number of stems: 1
    total number of isolated WC/wobble pairs: 3
    total number of atom-base capping interactions: 1
    total number of splayed-apart dinucleotides: 3
    total number of hairpin loops: 1
Uncaught exception 'Assertion failed' raised at [fncs_loop.c:1564]
aborting...

Do you know what is going on?

Thanks.

Best,
Honglue

Offline xiangjun

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Re: strange exception
« Reply #1 on: June 30, 2019, 09:05:03 pm »
Hi Honglue,

I can reproduce the reported issue. It is likely a bug in the code for ordering loop nucleotides in a special case. I will look into the issue and get it fixed (hopefully) shorty. Stay tuned.

Thanks for reporting.

Xiang-Jun
« Last Edit: June 30, 2019, 09:15:09 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline xiangjun

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Re: strange exception
« Reply #2 on: July 01, 2019, 07:41:30 pm »
Hi Honglue,

I've fixed the bug in the updated DSSR distribution on the download page. It was due to the relaxed definition of WC pairs to account for distorted geometry, which causes problems in a special case like yours.

Please have a try and report back how it goes. I'm planning to release DSSR tomorrow if no other issues pop up.

Best regards,

Xiang-Jun
« Last Edit: July 02, 2019, 12:51:18 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

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Re: strange exception
« Reply #3 on: July 01, 2019, 07:56:11 pm »
Hi Xiangjun,

It does work for this PDB structure. I am testing whether it works for the rest of my trajectory.

Best,
Honglue

Offline xiangjun

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Re: strange exception
« Reply #4 on: July 02, 2019, 12:50:54 pm »
Hi Honglue,

I've further polished the DSSR code, which will be released as v1.9.4-2019jul04. I am checking the new version against all nucleic-acid structures in the PDB to ensure it works as expected.

Please use the latest DSSR (v1.9.4-2019jul04) on the download page for tests on your trajectory, and report back any issues you may encounter.

Best regards,

Xiang-Jun
« Last Edit: July 02, 2019, 12:52:50 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

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Re: strange exception
« Reply #5 on: July 02, 2019, 12:55:16 pm »
The new version will be released on July 4th right?

Offline xiangjun

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Re: strange exception
« Reply #6 on: July 02, 2019, 12:58:57 pm »
It is already there in the download page and the new version will be made explicit on July 4. I may revise DSSR before the formal release note, though.

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

Offline lvelve0901

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Re: strange exception
« Reply #7 on: July 02, 2019, 01:01:11 pm »
Is it here?

Offline xiangjun

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Re: strange exception
« Reply #8 on: July 02, 2019, 01:03:51 pm »
Yes, just download and run x3dna-dssr -v to verify. Did not you download the previous DSSR update this way?

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

Offline lvelve0901

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Re: strange exception
« Reply #9 on: July 02, 2019, 01:06:31 pm »
Yes, I downloaded in this way. It is just it said the version is still may25 above that confuses me.

Offline xiangjun

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Re: strange exception
« Reply #10 on: July 02, 2019, 01:09:34 pm »
That confusion is understandable, and that's why I told you explicitly here. Ordinary users won't be bothered by the version "issue" at all.

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

Offline lvelve0901

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Re: strange exception
« Reply #11 on: July 02, 2019, 01:11:09 pm »
Gotcha. I am testing the new version on all of my trajectory now. I should be able to give you some update by end of today.

Offline lvelve0901

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Re: strange exception
« Reply #12 on: July 02, 2019, 11:09:56 pm »
Hi Xiangjun,

There are three pdb files in my trajectory that the new version DSSR (Jul4) cannot parse, it basically pops up the exact same error.

Best,
Honglue

Offline lvelve0901

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Re: strange exception
« Reply #13 on: July 02, 2019, 11:10:38 pm »
Command: x3dna-dssr -i=S_000331_021.pdb
Date and time: Tue Jul  2 23:22:26 2019
File name: S_000331_021.pdb
    no. of DNA/RNA chains: 1 [_=25]
    no. of nucleotides:    25
    no. of atoms:          796
    no. of waters:         0
    no. of metals:         0
    total number of base pairs: 9
    total number of multiplets: 1
    total number of helices: 1
    total number of stems: 1
    total number of isolated WC/wobble pairs: 3
    total number of atom-base capping interactions: 1
    total number of hairpin loops: 1
Uncaught exception 'Assertion failed' raised at [fncs_loop.c:1657]
aborting...

Time used: 00:00:00:01

Offline xiangjun

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Re: strange exception
« Reply #14 on: July 03, 2019, 11:28:16 am »
Hi Honglue,

Thanks for your follow-ups. These examples illustrate an intriguing situation in the identification of loops. Such cases never show up in the nucleic-acid-containing structures in the PDB. The DSSR source code is defensive with such special cases with an assert(), and that's what the error message is about.

Now that I have these examples to check against, it should be possible to devise a solution to all such cases. Stay tuned.

Best regards,

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

Offline lvelve0901

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Re: strange exception
« Reply #15 on: July 03, 2019, 11:36:50 am »
Hi Xiangjun,

Interesting, these trajectories were generated by Rosetta FARFAR which I believe utilizing a library from existing PDB. However, it seems it somehow generate some new conformational space that DSSR cannot recognize it, right?

Thank you so much for your help as always.

Best,
Honglue


Offline lvelve0901

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Re: strange exception
« Reply #16 on: July 03, 2019, 12:32:21 pm »
Hi Xiangjun,

By the way, I always keep using a very old version of DSSR which is v1.6.5-2017jan22. Now that since I am probably going to switch to this new version, could you please remind me of locations of the update log including all the details of modification? I couldn't find it in the website.

If you could briefly highlights some important changes I would even more appreciate.

Thank you.

Best,
Honglue

Offline xiangjun

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Re: strange exception
« Reply #17 on: July 03, 2019, 12:53:17 pm »
Check: http://forum.x3dna.org/rna-structures/dssr-release-history/

Overall, a newer version of DSSR can safely replace previous ones.

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

Offline xiangjun

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Re: strange exception
« Reply #18 on: July 04, 2019, 09:09:26 am »
Hi Honglue,

Happy The Fourth of July Holiday!

Please try the updated DSSR on the download page, and report back how it goes. I'll delay the next DSSR release until all known issues have been resolved.

Best regards,

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

Offline lvelve0901

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Re: strange exception
« Reply #19 on: July 04, 2019, 10:18:12 am »
Awesome. I am rerunning the new DSSR on my trajectory now and hopefully I will give you feedback this afternoon.

Happy 4th of July!

Offline xiangjun

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Re: strange exception
« Reply #20 on: July 05, 2019, 01:33:50 pm »
Hi Honglue,

I've further refined DSSR for handling special cases of loops, as in your cases. Please see an image of a fragment from your S_000020_289.pdb file. The 4-nt fragment has the following features:
  • The U6pA7 dinucleotide is on one side and the A19pU20 dinucleotide on the other
  • U6–A19 and A7–U20 form two Watson-Crick pairs
  • U6+A7 is a dinucleotide platform
  • Moreover, the four nts are co-planar, forming a tetrad (multiplet)
Is such an unusual arrangement expected?

Anyway, I believe the updated DSSR has solved all known issues. Please have a try and report back how it goes in your hand.

Best regards,

Xiang-Jun
« Last Edit: July 05, 2019, 02:03:17 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

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Re: strange exception
« Reply #21 on: July 05, 2019, 03:15:59 pm »
Hi Xiangjun,

So do you update a new version today? I am still running the version you upload yesterday on my trajectory. It seems that it took longer than I expected.

Best,
Honglue

Offline xiangjun

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Re: strange exception
« Reply #22 on: July 05, 2019, 03:25:52 pm »
Yes, I updated DSSR today. The previous DSSR version you're using should work: the "Uncaught exception 'Assertion failed'" message you reported earlier should be gone. Nevertheless, it is preferable to restart with the latest version.

Best regards,

Xiang-Jun
« Last Edit: July 05, 2019, 03:27:38 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline lvelve0901

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Re: strange exception
« Reply #23 on: July 05, 2019, 03:56:00 pm »
OK, I will restart using the version today.

Offline lvelve0901

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Re: strange exception
« Reply #24 on: July 07, 2019, 10:58:23 pm »
Hi Xiangjun,

It seems the new version (Jul8) works very well for all my trajectory for now.

By the way I am benchmarking your new version using a ribosomal structure (PDB 1FFK).

Here I attached the output using version 2017jan22 (x3dna-dssr-old) and 2019jul08 (x3dna-dssr).

Here is the output:


[hs189@summer:version] x3dna-dssr-old -i=1ffk.pdb -o=1ffk_old.json --more --json   

Processing file '1ffk.pdb'
    total number of base pairs: 1450
    total number of multiplets: 241
    total number of helices: 85
    total number of stems: 176
    total number of isolated WC/wobble pairs: 49
    total number of atom-base capping interactions: 211
    total number of splayed-apart dinucleotides: 327
    total number of hairpin loops: 66
    total number of bulges: 34
    total number of internal loops: 65
    total number of junctions: 35
-- kissing-loops in '1ffk.pdb', hairpin loops (#1/#3) have 2 interactions [#8, #9 ...]
    total number of A-minor (type I and II) motifs: 98
    total number of ribose zippers: 41
    total number of kink turns: 7
    total number of non-loop single-stranded segments: 31
    total number of kissing loops: 5

Time used: 00:00:00:50




[hs189@summer:version] x3dna-dssr -i=1ffk.pdb -o=1ffk.json --more --json

Processing file '1ffk.pdb'
    total number of nucleotides: 2828
    total number of amino acids: 3656
    total number of base pairs: 1428
    total number of multiplets: 238
    total number of helices: 83
    total number of stems: 175
    total number of isolated WC/wobble pairs: 50
    total number of atom-base capping interactions: 211
    total number of splayed-apart dinucleotides: 400
                        consolidated into units: 251
    total number of hairpin loops: 66
    total number of bulges: 37
    total number of internal loops: 65
    total number of junctions: 35
    total number of non-loop single-stranded segments: 29
-- kissing-loops in '1ffk.pdb', hairpin loops (#1/#3) have 2 interactions [#8, #9 ...]
    total number of kissing loops: 5
    total number of A-minor (types I and II) motifs: 99
    total number of eXtended A-minor (type X) motifs: 55
    total number of ribose zippers: 41
    total number of kink turns: 8

Time used: 00:00:01:17



For example, it seems the new version detect less base pairs, less multiplets, is that because you adjust the criteria for base pair or something?

If you think this post should be in a separate topic, could you please help move it to a proper place?

Best,
Honglue

 

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.