Recent Posts

51

General discussions (Q&As) / Re: All Possible Base Pairs

« Last post by xiangjun on June 09, 2024, 10:34:29 pm »

Hi Parivash,

Thanks for your interest in using 3DNA. The find_pair -p command should give you a list of all pairs, canonical or not. Please provide a concrete example to illustrate what base pairs are missing.

As for the availability of x3dna-dssr, please see the post "No more grant funding for 3DNA/DSSR" (http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/). You could use http://skmatics.x3dna.org to analyze/visualize a structure using x3dna-dssr.

Hope this helps.

Xiang-Jun

52

General discussions (Q&As) / All Possible Base Pairs

« Last post by pfeyzi on June 09, 2024, 07:11:36 pm »

Dear Dr. Lu,
I hope this message finds you well.
I am currently using x3DNA to identify base pairs in my PDB files. I have been using the command
"find_pair -p X.pdb stdout | analyze stdin"
which provides me with the strongest base pairs for each residue. However, I am interested in identifying all possible base pairs, including both canonical and non-canonical pairs, regardless of their strength.
Is there a way to modify the command or use a different tool within x3DNA to obtain a comprehensive list of all possible base pairs for each residue? or can we change its constraints to include all pairs?
Additionally, I found in the new version of x3DNA, x3dna-dssr tool is not available. Is it possible to download the versions which includes that?
Thanks you so much,
Parivash

53

MD simulations / Re: Gromacs missing ' P ' atom

« Last post by xiangjun on May 27, 2024, 06:41:08 pm »

No, it is for information only: i.e., the first nucleotide (DG1) does not have the phosphate group.

54

MD simulations / Gromacs missing ' P ' atom

« Last post by mouxuank on May 27, 2024, 04:03:40 am »

When I used "find_pair 0.pdb | analyze" to analyze the Gromacs simulation output pdb file, I got the following tips, whether this affects the result and how I should solve the problem.

'''
handling file <0.pdb>

Time used: 00:00:00:00
missing ' P  ' atom : residue name ' DG', chain  , number [   1 ]
missing ' OP1' atom : residue name ' DG', chain  , number [   1 ]
missing ' OP2' atom : residue name ' DG', chain  , number [   1 ]
missing ' P  ' atom : residue name ' DG', chain  , number [   1 ]
missing ' OP1' atom : residue name ' DG', chain  , number [   1 ]
missing ' OP2' atom : residue name ' DG', chain  , number [   1 ]
missing ' P  ' atom : residue name ' DG', chain  , number [   1 ]
missing ' P  ' atom : residue name ' DG', chain  , number [   1 ]

Time used: 00:00:00:01
'''

55

RNA structures (DSSR) / Re: DSSR Basic Licence Application: Seeking Status Update and Assistance

« Last post by xiangjun on February 20, 2024, 06:02:31 pm »

Hi Junkai,

Thanks for the update. Getting DSSR-Basic, Academic license has been very straightforward from past experiences. As I heard from the CTV, your application has triggered a review of the license policy, and thus the delay. I am not sure of the exact details, but being patient seems to the best thing that can be done.

Let's stop this thread and put future communications via email.

Best regards,

Xiang-Jun

56

RNA structures (DSSR) / Re: DSSR Basic Licence Application: Seeking Status Update and Assistance

« Last post by junkaiWang on February 20, 2024, 01:15:50 pm »

Dear Xiang-Jun,

I'm writing to provide you with an update on my recent efforts to seek assistance.

Following the contact information provided on the Columbia Technology Venture (CTV) website, I reached out via email to techtransfer@columbia.edu in hopes of gaining support and guidance. Unfortunately, I have yet to receive a response from them. I have thoroughly checked my email records and ensured that the address was correctly spelled. I look forward to my project being able to use DSSR as soon as possible.

Thank you once again for your time and attention.

Best regards,

Junkai

57

RNA structures (DSSR) / Re: DSSR Basic Licence Application: Seeking Status Update and Assistance

« Last post by junkaiWang on February 19, 2024, 07:08:06 am »

Dear Xiang-Jun,

I am very sorry to interrupt you again. Unfortunately, I still haven't received my DSSR license, and I believe it may be due to the weekend or some other change. I sincerely hope to receive it soon.Thanks again!

Best regards,

Junkai

58

RNA structures (DSSR) / Re: DSSR Basic Licence Application: Seeking Status Update and Assistance

« Last post by xiangjun on February 16, 2024, 09:05:42 am »

Hi Junkai,

Thanks for your interest in purchasing a DSSR Basic Academic License. Sorry for the unexpected delay in response from the CTV. I've communicated with people in charge, and hopefully the issue will be resolved shortly.

Best regards,

Xiang-Jun

59

RNA structures (DSSR) / DSSR Basic Licence Application: Seeking Status Update and Assistance

« Last post by junkaiWang on February 16, 2024, 03:34:35 am »

Dear Xiangjun,

I hope this message finds you well. I'm writing to follow up on my recent application for the DSSR Basic Licence,  which was submitted by my supervisor(Lijun Quan) on 9th February, . As of now, I haven't received any confirmation or updates regarding the status of my application. Could you kindly provide me with some information on the next steps or any additional actions I might need to take to facilitate the process?

Thank you very much for your attention and assistance. I truly appreciate your help in this matter.

With best regards
Junkai

60

RNA structures (DSSR) / Re: 2D DNA structure

« Last post by luka86 on February 05, 2024, 09:36:24 am »

Thank you, but it seems that there is no free version of dssr. Is there any option to parse the x3dna output or some other way that is free of charge?
Thanks in advance.