Messages

1

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

« 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

2

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

« 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

3

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

« 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

4

RNA structures (DSSR) / Re: How does 3dna-dssr convert the atomic coordinates from PDB files into its output

« on: February 04, 2024, 02:28:43 am »

Hi Xiangjun,

Thank you for your patient reply. I now understand the issue.
I have one final question:
what are the criteria for selecting the origin and XYZ axis vectors for the coordinate system?

Best regards,
Junkai Wang

5

RNA structures (DSSR) / Re: How does 3dna-dssr convert the atomic coordinates from PDB files into its output

« on: February 02, 2024, 07:39:46 am »

Hi Xiangjun,

I apologize for not providing specific details when I asked my question. Below, I will present my process and concerns.

I obtained the RNA annotation dictionary 'annot' using x3dna-dssr --json -i=2tob.cif.

Then, I filtered(filter(lambda x: x['nt_type'] == 'RNA', annot['nts']) the 'annot' dictionary to retain only the RNA content nt_annot.

I can retrieve information about the target base by using nt_annot['nt_id'].
For example, on base with ID 2tob.A.10, the coordinates in nt_annot['2tob.A.10'] are as follows:
C5' atom coordinate       C5prime_xyz: [-1.405, 8.313, 1.694]
P atom coordinate          P_xyz: [1.204, 8.473, 2.116]

However, the atomic coordinates for this base in the PDB file are as follows. The same situation exists for other bases of this RNA.
ATOM    191  P     U A  10     -16.156  -3.688 -12.208  1.00  0.30           P 
ATOM    195  C5'  U A  10     -15.795  -3.890 -14.824  1.00  0.34           C 

Clearly, they are different. Therefore, I would like to know what processing has been done on them(from PDB_xyz to DSSR_xyz).
I hope I've stated my question clearly.

Best regards,
Junkai Wang

6

RNA structures (DSSR) / How does 3dna-dssr convert the atomic coordinates from PDB files into its output

« on: February 01, 2024, 07:21:19 am »

Hi Xiangjun,

I encountered an issue while analyzing RNA structures using the 3dna-dssr program: I noticed that the XYZ coordinates of atoms such as base C5' in the output results are not consistent with those in the PDB file, indicating that some transformation has been applied. I found that there seems to be a relative coordinate system between base pairs in the output file, and I attempted to use it for conversion, but the results did not meet my expectations. Could you please clarify how the coordinates in the PDB file are transformed into the format used in the program's output?