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Questions and answers => RNA structures (DSSR) => Topic started by: jyvdf3asdg2 on March 04, 2013, 01:59:44 pm

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Title: Bug report of DSSR beta
Post by: jyvdf3asdg2 on March 04, 2013, 01:59:44 pm

Hi xiangjun,

Great program. Looks to find structural motifs really well.

I ran in to a bit of a problem though, DSSR seems to hang on 2VQE. BFactors.dat and the pairs.pdb files are generated, but the program just hangs thereafter. I've processed all the other large ribosome structures with no problems, but this one seems to give it a hard time. I've tried stdout and writing out, neither work.

I've tried re-downloading the PDB, as well. It works fine for 3DNA.

Thanks

Title: Re: Bug report of DSSR beta
Post by: jyvdf3asdg2 on March 04, 2013, 02:39:49 pm

Hi xiangjun,

Caught a few C-exceptions on PDB's that should all have base pairs:

Code: [Select]

--------------PDB ID: 1N3E --------------

total number of helices: 1

total number of stems: 6
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:215]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 1QCU --------------

total number of helices: 10

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:191]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 1QLN --------------

total number of helices: 2

total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 1Y26 --------------

total number of helices: 5

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:191]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2DLC --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2GCV --------------

total number of helices: 5

total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2H0S --------------

total number of helices: 5

total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2H0W --------------

total number of helices: 5

total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2NZ4 --------------
Residue [E.G1] has canonical ring atoms missed (8 vs 9)

total number of helices: 22

total number of stems: 40
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 2PXB --------------

total number of helices: 2

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 2PXD --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXE --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXF --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXK --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXL --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXP --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXQ --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXT --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXU --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2PXV --------------

total number of helices: 2

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2V3C --------------
N.G215 0.10

total number of helices: 6

total number of stems: 13
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 2VJU --------------

total number of helices: 4

total number of stems: 6
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2XM3 --------------

total number of helices: 12

total number of stems: 18
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2XMA --------------

total number of helices: 8

total number of stems: 12
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 2XO6 --------------

total number of helices: 6

total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2XQC --------------

total number of helices: 6

total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 2ZUE --------------

total number of helices: 2

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 2ZUF --------------

total number of helices: 3

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3ADD --------------

total number of helices: 6

total number of stems: 10
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3AGV --------------

total number of helices: 4

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3AM1 --------------

total number of helices: 3

total number of stems: 6
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3C1B --------------

total number of helices: 4

total number of stems: 10
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:02
-------------------------------------
--------------PDB ID: 3CC2 --------------

total number of helices: 106

total number of stems: 179
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:08
-------------------------------------
--------------PDB ID: 3DD2 --------------

total number of helices: 2

total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3EGZ --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3FOZ --------------

total number of helices: 5

total number of stems: 9
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3H8X --------------
Residue [C.DA279] has canonical ring atoms missed (8 vs 9)

total number of helices: 2

total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3HAX --------------
F.FHU7 0.16

total number of helices: 2

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3HJW --------------
E.FHU10 0.15

total number of helices: 2

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3HXO --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 3LQX --------------

total number of helices: 2

total number of stems: 3
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3LWP --------------

total number of helices: 2

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3LWR --------------

total number of helices: 2

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3LWV --------------

total number of helices: 2

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3MNN --------------
atom 12042: [RU@F.RU2001] has > 6 bonds
atom 12068: [RU@G.RU2001] has > 6 bonds
atom 12094: [RU@H.RU2001] has > 6 bonds

total number of helices: 5

total number of stems: 8
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:02
-------------------------------------
--------------PDB ID: 3MXH --------------

total number of helices: 4

total number of stems: 7
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 3RW6 --------------
H.CCC62 0.10
F.CCC62 0.10

total number of helices: 4

total number of stems: 10
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3U4M --------------

total number of helices: 4

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3U56 --------------

total number of helices: 4

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 3UMY --------------

total number of helices: 4

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 3UTB --------------

total number of helices: 2

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 3ZGZ --------------

total number of helices: 6

total number of stems: 10
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 4AQ7 --------------

total number of helices: 6

total number of stems: 10
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 4ARC --------------

total number of helices: 3

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 4ARI --------------

total number of helices: 4

total number of stems: 4
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 4AS1 --------------

total number of helices: 3

total number of stems: 5
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 4ATO --------------

total number of helices: 1

total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:01
-------------------------------------
--------------PDB ID: 4HQU --------------

total number of helices: 2

total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------
--------------PDB ID: 4HQX --------------

total number of helices: 3

total number of stems: 2
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:771]
aborting...

Time used: 00:00:00:00
-------------------------------------

Title: Re: Bug report of DSSR beta
Post by: xiangjun on March 04, 2013, 02:48:19 pm

Hi,

Thanks for using DSSR, and reporting back the issues you experienced. I will look into them and release an updated version shortly. Stay tuned  :D

Xiang-Jun

Title: Re: Bug report of DSSR beta
Post by: xiangjun on March 06, 2013, 12:05:45 pm

Hi,

All the bugs you reported should have been fixed, and DSSR beta-r02-on-20130306 released. Please have a try and report back how it goes.

As you may notice, I have split the thread from the original DSSR announcement post. I also put the long list of buggy cases reported in your second post into the code tag for easy browsing.

Do not be shy in bringing up more bugs --- the more, the merrier!  :D

Xiang-Jun

Title: Re: Bug report of DSSR beta
Post by: jyvdf3asdg2 on March 08, 2013, 04:33:52 pm

Hi,

Thanks for fixing those bugs! Hope you don't mind if I bring you some more bugs with the revised version:

Code: [Select]

----Processing: 1BDN -------

total number of multiplets: 0
Uncaught exception 'Assertion failed' raised at [fncs_helix.c:911]
aborting...

Time used: 00:00:00:01

----Processing: 1QP5 -------

total number of multiplets: 0

total number of helices: 1

total number of stems: 1
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...

Time used: 00:00:00:01

----Processing: 1VTD -------

total number of multiplets: 0

total number of helices: 1

total number of stems: 1
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...

Time used: 00:00:00:00

----Processing: 2J00 -------

total number of multiplets: 108

total number of helices: 68

total number of stems: 101
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...

Time used: 00:00:00:16

----Processing: 2J02 -------

total number of multiplets: 106

total number of helices: 67

total number of stems: 98
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...

Time used: 00:00:00:16

----Processing: 2ZJR -------

total number of multiplets: 170

total number of helices: 117

total number of stems: 180
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...

Time used: 00:00:00:19

----Processing: 3OHK -------
A.G1332 0.10
A.A2346 0.10

total number of multiplets: 218

total number of helices: 108

total number of stems: 177
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...

Time used: 00:00:00:13

----Processing: 3OHZ -------
A.A2346 0.11

total number of multiplets: 208

total number of helices: 111

total number of stems: 178
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...

Time used: 00:00:00:13

----Processing: 3OI0 -------

total number of multiplets: 88

total number of helices: 63

total number of stems: 89
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...

Time used: 00:00:00:20

Found no basepairs for: 3OI0
----Processing: 3OI1 -------

total number of multiplets: 210

total number of helices: 112

total number of stems: 178
Uncaught exception 'Assertion failed' raised at [fncs_dssr.c:161]
aborting...

Time used: 00:00:00:12

----Processing: 6CRO -------

total number of multiplets: 0
Uncaught exception 'Assertion failed' raised at [fncs_helix.c:911]
aborting...

Time used: 00:00:00:01

Thanks!

Title: Re: Bug report of DSSR beta
Post by: xiangjun on March 08, 2013, 04:42:50 pm

I wholeheartedly welcome bug reports, and this latest is of no exception :). I'll get them fixed shortly -- hopefully by tomorrow. With the next release, the program would be quite robust, I believe.

Have a great weekend.

Xiang-Jun

Title: Re: Bug report of DSSR beta
Post by: xiangjun on March 09, 2013, 04:06:55 pm

Following my previous post, I've just released DSSR beta-r03-on-20130309. I tested this version against all nucleic-acid-containing structures in the PDB, so all the bugs you reported yesterday should have been fixed. I was actually approaching the end of such an extensive tests when I say your post, and your reported cases were already handled at that time.

It's worthy noting that some of the DSSR buggy cases are due to problematic data quality of the corresponding PDB entries. For example, 1bdn (http://www.rcsb.org/pdb/explore/explore.do?structureId=1bdn) apparently have two structures overlapped (with 4 chains instead of 2) -- check the structure with PyMOL or Jmol, and you will seem my point.

While more bugs are bound to be uncovered, and further refinements are necessary, I am confident to say that DSSR (beta-r03-on-20130309) is robust enough for real-world applications. As always, do not be shy to report back any issues you encounter.

Xiang-Jun

Title: Re: Bug report of DSSR beta
Post by: jyvdf3asdg2 on March 09, 2013, 09:24:35 pm

Thanks Xiang-Jun!

I definitely know the type of structures you are talking about. Pymol has a hard time processing them as well.

Title: Re: Bug report of DSSR beta
Post by: MarcParisien on March 18, 2013, 12:16:28 pm

Hi Dr. Lu,

  3dna-dssr is a great program!

  I get a "segmentation fault" from the 64-bits unix version of beta-r05-on-20130316. The PDB file which triggers this is 2a64-1 (the first and only "biological assembly"). Works well on other classics, like 2k4c-1 and 1gid-1.


  Thanks for looking into this,
    Marc.

Title: Re: Bug report of DSSR beta
Post by: xiangjun on March 18, 2013, 01:33:30 pm

Hi Marc,

Thanks for trying out DSSR and reporting back a bug with the 64-bits unix version of beta-r05-on-20130316 on PDB entry 2a64. I've verified the bug and will get it fixed ASAP.

I've also tried the same 2a64 entry with the Mac OS X version without the reported problem. Since the "Segmentation fault (core dumped)" occurs after the output of "total number of junctions: 4", it is likely due to the ribose zipper detection function recently added into DSSR.

In any event, keep testing and report back any further issues you encounter. Also stay tuned for the next release! :)

Xiang-Jun

Title: Re: Bug report of DSSR beta
Post by: xiangjun on March 19, 2013, 12:36:23 am

Hi Marc,

I've just released DSSR beta-r06-on-20130319 which should have fixed the "segmentation fault" bug for PDB entry 2a64. I've also taken this opportunity to update the -h (--help) message.

Have a try and report back how it goes!

Xiang-Jun

Title: Re: Bug report of DSSR beta
Post by: febos on December 03, 2013, 05:28:19 am

Good Afternoon Dr. Xiang-Jun Lu.

I've noticed a little bug in your program, seems like you forgot an opening bracket ('[') in fields of helices and stems:

Code: [Select]

   2 10.A.G.2.        10.A.C.37.       G-C WC           19-XIX    cWW cW-W
        bp1_pars:      -1.29    -0.35    -0.04    -1.33    -0.11    -5.26]
       step_pars:      -0.60    -1.65     3.04    -1.46    22.01    44.24]
       heli_pars:      -3.36     0.63     2.07    27.31     1.81    49.19]
        bp2_pars:       0.37     0.21    -0.06     1.55     2.78    -7.23]
       C1'-based: rise=3.96     twist=34.6     h-rise=2.19     h-twist=39.1
It's in the latest release of DSSR

Best regards,
Eugene

Title: Re: Bug report of DSSR beta
Post by: xiangjun on December 03, 2013, 09:21:35 am

Hi Eugene,

Good catch. I will get it fixed in the next beta release soon.

Thanks,

Xiang-Jun

Title: Re: Bug report of DSSR beta
Post by: xiangjun on December 03, 2013, 03:24:30 pm

Hi Eugene,

The bug has been fixed in DSSR beta-r27-on-20131203. Now the output looks like below:

Code: [Select]

        bp1_pars:  [-1.59    0.32     -0.26    1.95     -3.60    -43.73]
       step_pars:  [2.96     -1.31    3.22     -5.29    6.77     34.80]
       heli_pars:  [-3.00    -5.49    2.46     11.10    8.68     35.82]
        bp2_pars:  [-2.37    -0.60    0.11     4.67     -7.75    -2.95]
Please have a try, and keep reporting back any bugs you may find!

Thanks,

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