Recent Posts

1

RNA structures (DSSR) / Re: x3dna-dssr -h no response

« Last post by xiangjun on January 15, 2021, 09:53:57 pm »

Hi,

• The 3DNA suite of programs (up to v2.4) has been superseded by DSSR. See the Overview PDF, especially Section 1.4 DSSR vs. 3DNA vs. SCHNAaP/SCHNArP.
• DSSR is licensed by Columbia University. It is available only through the website http://innovation.columbia.edu/technologies/CU20391
• 3DNA v2.4 (along with SCHNAaP/SCHNArP) is still available for downloaded from this Forum, but it is on longer developed/supported.

Hope this helps.

Xiang-Jun

2

RNA structures (DSSR) / x3dna-dssr -h no response

« Last post by rvandamm on January 15, 2021, 09:05:30 pm »

Hello all. I just downloaded and installed x3dna-v2.4  and am running it in ubuntu on the linux susbystem for windows 10. I believe I set everything up correctly because find_pair -h works for me. However when I go through the manual and try the commands x3dna-dssr -h or any x3dna-dssr command it returns "x3dna-dssr: command not found". I don't know what I am doing wrong at this point and I am trying to be able to get the dot bracket notation for PDBs for RNAs of interest, I'm still very new at this so any helpful advice would be appreciated. Thank you.

3

RNA structures (DSSR) / Re: DSSR eta-base theta-base

« Last post by xiangjun on January 09, 2021, 07:19:44 pm »

Hi Cathy,

Happy 2021!

Following your request, I've updated DSSR so that the JSON output for pseudo-torsion angles eta_base and theta_base would be "null" instead of 0.0 when they cannot be calculated. I have also refined DSSR to account for chain breaks while calculating all pseudo torsions.

The updated DSSR (v2.2.1) will be available from the Columbia Technology Ventures (CTV) website, presumably by early next week. As you may know, DSSR is now licensed by Columbia University.

Best regards,

Xiang-Jun

4

RNA structures (DSSR) / DSSR eta-base theta-base

« Last post by cllawson on January 09, 2021, 09:05:52 am »

Dear Xiangjun, 

Wishing you a Happy New Year! 

I have a request regarding DSSR json output for pseudotorsion angles.  I noticed that when backbone is present but no base has been modelled,  eta-base and theta-base values are listed as 0.0 and 0.0. Could you instead assign "null" as done for other pseudotorsion angles that cannot be calculated?  (e.g. eta for 1st residue in a polymer always shows as "null").  PDB ids where I noticed this issue: 6g4s (no bases deposited for entire structure), and 6sg9 (some residues with bases, others without).  Using: DSSR v1.9.10-2020apr23.

Thanks,

Cathy

5

General discussions (Q&As) / Re: How 3DNA calculate base overlapping?

« Last post by xiangjun on December 27, 2020, 02:28:29 pm »

Please read the 2003 3DNA paper and the 2015 DSSR paper.

Xiang-Jun

6

DNA/RNA-protein interactions (SNAP) / Re: How to download the SNAP code?

« Last post by xiangjun on December 27, 2020, 02:25:50 pm »

A quick note: SNAP has been integrated into DSSR, as of v2.2, and available for download from CTV.

Xiang-Jun

7

General discussions (Q&As) / How 3DNA calculate base overlapping?

« Last post by jzhang71 on December 17, 2020, 09:42:59 pm »

Hi,

Do you know how 3DNA calculate the overlapping area of bases when calculating the base stacking? By Monte Carlo method or there is an analytical solution? Is there a analytical solution of purine-purine stacking (since purine have two rings)?

Thank you very much!

8

FAQs / Re: Where to download x3DNA

« Last post by xiangjun on December 08, 2020, 05:34:07 pm »

Hi Pawel,

You should now be able to see the Download section.

There is a lag from the time an account is activated to it being granted download access. The rules for registration/download have been tightening up to keep the Forum spam free, and to serve legitimate users only. I have updated the FAQ entry "How to make the best use of the Forum" to make the process more transparent.

Best regards,

Xiang-Jun

9

FAQs / Where to download x3DNA

« Last post by gosc on December 08, 2020, 04:05:02 pm »

Dear Sir,
I followed the instructions to register, got the confirmation link and logged in apparently properly, yet I do not see the "download" link as described in the instruction.
Digging over the forum I have found another link but the target page announced that it either doesn't exists or I have no access to it.
Is the program still available?
Thanks
Pawel

10

DNA/RNA-protein interactions (SNAP) / Re: Difference between pi-stacking and pi-pair in SNAP

« Last post by akakios on December 07, 2020, 08:00:00 pm »

Dr. Xiang-Jun Lu,

Maybe now I got what I wanted to know. I appreciate it. Thank you.

Takayuki