Recent Posts

1

General discussions (Q&As) / Re: building circular DNA

« Last post by xiangjun on July 16, 2019, 12:06:01 pm »

I understood that you have been "trying to create a DNA ring system". 3DNA does not have a direct solution to this problem, neither will it likely in the general sense.

You may give NAB a try. If you find a way, please post back so other viewers may benefit.

Best regards,

Xiang-Jun
 

2

Feature requests / MOVED: building circular DNA

« Last post by xiangjun on July 16, 2019, 11:56:46 am »

This topic has been moved to General discussions (Q&As).

http://forum.x3dna.org/index.php?topic=862.0

3

General discussions (Q&As) / Re: building circular DNA

« Last post by x3dna_test on July 16, 2019, 01:28:56 am »

Hi Xiangjun,

I am just trying to create a DNA ring system and then do some simulations to study some properties.
Am not sure what parameters will be good as I do not have any experimental data.

4

General discussions (Q&As) / Re: building circular DNA

« Last post by xiangjun on July 15, 2019, 09:36:33 pm »

Hi,

I'm not sure I fully understand your question in a practical sense. Please be specific.

The 3DNA rebuild can generate any structure (at the base-pair level) with a set of prescribed base-pair and step parameters. It's really up to the user to build what they want.

Best regards,

Xiang-Jun
 

5

General discussions (Q&As) / building circular DNA

« Last post by x3dna_test on July 15, 2019, 06:11:48 pm »

Hi Xiangjun and All,

I am just wondering is it possible to build a circular DNA? I have seen one can analyse circular DNA with x3DNA but not sure how to build them and what parameters to be used.
Thanks.

6

RNA structures (DSSR) / Re: strange exception

« Last post by xiangjun on July 08, 2019, 02:21:16 pm »

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

Glad to hear that the updated version works. I've just released DSSR v1.9.4-2019jul08.

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:
...
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?

DSSR has been under continuous development and delivery. I maintain an extensive test set that includes all known buggy cases (such as your attached examples in this thread). For each release, I test DSSR against all nucleic-acid structures in the PDB to ensure that it does not crash. Except for boundary cases, DSSR is stable from version 1.0 and backward compatible, especially with the JSON output. I am confident that DSSR is a solid software product, with robust performances in real-world applications.

If you are interested in knowing the details between the two versions you tested, please start a new thread. Please provide concrete examples (base pairs, multiplets, etc.) where the differences really bother you.

Best regards,

Xiang-Jun

7

RNA structures (DSSR) / Re: strange exception

« Last post by lvelve0901 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

8

RNA structures (DSSR) / Re: strange exception

« Last post by lvelve0901 on July 05, 2019, 03:56:00 pm »

OK, I will restart using the version today.

9

RNA structures (DSSR) / Re: strange exception

« Last post by xiangjun 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

10

RNA structures (DSSR) / Re: strange exception

« Last post by lvelve0901 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