Recent Posts

91

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

92

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

93

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

94

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.

95

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

« Last post by xiangjun on February 04, 2024, 11:19:43 am »

Code: [Select]

what are the criteria for selecting the origin and XYZ axis vectors for the coordinate system?

It helps that you reads 3DNA/DSSR-related publications, and report back what you find.

96

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

« Last post by junkaiWang 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

97

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

« Last post by xiangjun on February 02, 2024, 09:35:33 pm »

Hi Junkai,

Thanks for your follow-up. Now your question can be answered, using C5' atom as an example:

ATOM    195  C5'  U A  10     -15.795  -3.890 -14.824  1.00  0.34           C  
C5' atom coordinate       C5prime_xyz: [-1.405, 8.313, 1.694]

C5prime_xyz is the original C5' atomic coordinates [-15.795  -3.890 -14.824] expressed in the local base reference frame,

Code: [Select]

{"rmsd":0.013,"origin":[-7.546,-2.079,-13.202],
              "x_axis":[-0.071,0.233,0.970],
              "y_axis":[-0.997,0.020,-0.078],
              "z_axis":[-0.037,-0.972,0.231],
"quaternion":[0.543,0.412,-0.464,0.566]}


dd = [-15.795  -3.890 -14.824] - [-7.546,-2.079,-13.202] = [-8.249  -1.811  -1.622]

dd * [ -0.071  -0.997  -0.037
        0.233   0.020  -0.972
        0.970  -0.078   0.231 ] = [-1.4096   8.3145   1.6908]

The slight difference between [-1.4096   8.3145   1.6908] and [-1.405, 8.313, 1.694] is due to round off errors.

Hope this helps.

Xiang-Jun

PS. Which version of DSSR are you using?

98

Feature requests / MOVED: 2D DNA structure

« Last post by xiangjun on February 02, 2024, 12:14:28 pm »

This topic has been moved to RNA structures (DSSR).

http://forum.x3dna.org/index.php?topic=1020.0

99

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

« Last post by xiangjun on February 02, 2024, 12:13:19 pm »

Hi Luka,

Thanks for attaching file AATAAA_dna.pdb (no need to copy-and-paste the content). DSSR does what you want, as shown below:

Code: [Select]

x3dna-dssr -i=AATAAA_dna.pdb -o=AATAAA_dna.out

# dssr-2ndstrs.dbn
>AATAAA_dna nts=16 [AATAAA_dna] -- secondary structure derived by DSSR
GCGCGAATAAACGCGC
(((((......)))))

# dssr-2ndstrs.ct
   16 ENERGY = 0.0 [AATAAA_dna] -- secondary structure derived by DSSR
    1 G     0     2    16     1
    2 C     1     3    15     2
    3 G     2     4    14     3
    4 C     3     5    13     4
    5 G     4     6    12     5
    6 A     5     7     0     6
    7 A     6     8     0     7
    8 T     7     9     0     8
    9 A     8    10     0     9
   10 A     9    11     0    10
   11 A    10    12     0    11
   12 C    11    13     5    12
   13 G    12    14     4    13
   14 C    13    15     3    14
   15 G    14    16     2    15
   16 C    15     0     1    16

It generates output file AATAAA_dna.out, and a few auxiliary files including dssr-2ndstrs.ct and dssr-2ndstrs.dbn which are all attached.

See the post [No more grant funding for 3DNA/DSSR](http://forum.x3dna.org/site-announcements/no-more-grant-funding-for-3dnadssr/).

Xiang-Jun

100

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

« Last post by luka86 on February 02, 2024, 09:20:33 am »

Thank you, I am sending the file in the attachment of the PDB file and also of the .out file that I got. But I am on mac, I am not sure if I have successfully uploaded the files.