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31
General discussions (Q&As) / Re: 3DNA manual
« Last post by xiangjun on July 28, 2021, 09:16:09 am »
Check the $X3DNA/doc folder.


Remember to post specific questions in a new thread with a clear subject line.

Reading posts linked at "Netiquette" at the upper-left corner of the Forum should help.

Best regards,

Xiang-Jun
32
Hi chen long,

Quote
1. After I got the academic license through Columbia University, I downloaded two versions of dssr-basic for linux and windows. But the windows version of the exe installation package can't open all the time. I have tried it on several computers with win7 and win10, but it doesn't work, so I would like to ask Dr. Lu why.

This is the first time I've heard of problems installing DSSR on Windows and Linux.

I do not understand what you mean by "But the windows version of the exe installation package can't open all the time." Does it work sometime? If so, when and under what condition? What do you mean by "it doesn't work"? Please provide screenshots to illustrate unambiguously the issues you experienced.

Quote
2. The files in the linux installation package are not in tar.gz format. I don't know how to install it. Could you please tell me. Or is there an installation method I haven't found? I did find it for a long time.

Then what format do you have from CTV download set? How long have you tried to find any other installation format?

It is fashionable these days to discuss the reproducibility of scientific publications. It's also crucial to ask questions in a consistent manner.

Best regards,

Xiang-Jun
33
DSSR Pro can do it and more.

Xiang-Jun
34
I am currently working on a project that uses 1o15.pdb
It is a structure where RNA and theophylline molecules are bound. I want to mutate the bases of different sites of RNA at the same time.
For example, ACGUACGUACGU mutates positions 2-6 and mutates more than one base to ANNNNNGUACGU, and creates a new PDB file with 45 sequences. Can mutate_bases in X3DNA achieve this function?or it can use in dssr-basic. Thank you for your reply!

35
Hello! I would like to share with you some recent issues regarding the use of DSSR. First of all, thank you for your great contributions to DSSR and X3DNA, which have helped many scholars and are free for academic institutions to use. My question is as follows:
1. After I got the academic license through Columbia University, I downloaded two versions of dssr-basic for linux and windows. But the windows version of the exe installation package can't open all the time. I have tried it on several computers with win7 and win10, but it doesn't work, so I would like to ask Dr. Lu why.
2. The files in the linux installation package are not in tar.gz format. I don't know how to install it. Could you please tell me. Or is there an installation method I haven't found? I did find it for a long time. So please let me know, thank you very much.  :D


Best wishes
chen long
36
General discussions (Q&As) / 3DNA manual
« Last post by chenlong on July 28, 2021, 01:33:34 am »
Hello, can I get a  the operation manual of x3DNA, 2.4  WINDOW version? I find but no result in this forum,sorry .
37
RNA structures (DSSR) / Re: how to repair a DNA model
« Last post by xiangjun on July 27, 2021, 11:48:48 am »
Please provide some background info and a concrete example to illustrate unambiguously what you want to achieve.

Thanks,

Xiang-Jun
38
RNA structures (DSSR) / how to repair a DNA model
« Last post by Garyren on July 27, 2021, 11:20:38 am »
I have a DNA model, however there are many broken chains in this model. I wonder if your DSSR can repair the broken DNA model?

39
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by xiangjun on July 23, 2021, 06:17:33 pm »
Quote
Yes, I tried and finally manage to color differently at each nucleotide blocks.

Glad to know that you have managed to color nucleotide blocks as desired. This is an important first step for later on speed optimizations.

Quote
But it is quite slow since it make all individual block object for every nucleotide.


How many colors do you want to have? Grouping nucleotides with the same color should speed up the process. It is now a matter of PyMOL selection syntax to play with.

Quote
And also it print lots of warning messages during the run.
I can't locate the origin of this warning.
PyMOL>dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'

I cannot reproduce the warning messages. Let's not worry about them right now.

Best regards,

Xiang-Jun

40
RNA structures (DSSR) / Re: Color each block nucleotide at each locations
« Last post by spark159 on July 23, 2021, 05:56:15 pm »
And also it print lots of warning messages during the run.
I can't locate the origin of this warning.



Time used: 00:00:00:00
PyMOL>dssr_block (chain J and resi 56), block_color='N:[1.0 0.393 0.0]'

Processing file '/tmp/tmpinhy880j.pdb'
   more than one < P  > atoms in J.DG56
   *****the first match is used*****
   more than one < OP1> atoms in J.DG56
   *****the first match is used*****
   more than one < OP2> atoms in J.DG56
   *****the first match is used*****
   more than one < O5'> atoms in J.DG56
   *****the first match is used*****
   more than one < C5'> atoms in J.DG56
   *****the first match is used*****
   more than one < C4'> atoms in J.DG56
   *****the first match is used*****
   more than one < O4'> atoms in J.DG56
   *****the first match is used*****
   more than one < C3'> atoms in J.DG56
   *****the first match is used*****
   more than one < O3'> atoms in J.DG56
   *****the first match is used*****
   more than one < C2'> atoms in J.DG56
   *****the first match is used*****
   more than one < C1'> atoms in J.DG56
   *****the first match is used*****
   more than one < N9 > atoms in J.DG56
   *****the first match is used*****
   more than one < C4 > atoms in J.DG56
   *****the first match is used*****
   more than one < C8 > atoms in J.DG56
   *****the first match is used*****
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.