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91
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
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
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
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
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
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 »
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.
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Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University