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1

FAQs / How to make the best use of the Forum

« Last post by xiangjun on May 19, 2017, 11:35:45 am »

• Register to download the 3DNA software (including DSSR and SNAP) and post questions. Non-registered viewers can only read existing posts; they will not see the Downloads section and they are not allowed to post on the Forum. Over the years, I've received many private emails asking for help, and those users have been (mostly) responded with the following canned message:
  
  

  Thanks for your interest in using 3DNA. Please be aware that for the benefit of the 3DNA-user community at large, I do not provide private email support; the 3DNA Forum (http://forum.x3dna.org/) has been created specifically for open discussions of all 3DNA-related issues. In other words, *any* 3DNA-associated questions are welcome and should be directed there. Specifically, please do *not* be shy in sharing openly and concretely difficult experiences you may have in installing or using the software.
  
  By asking your questions on the public 3DNA Forum, you are not only benefiting yourself but also the user community. I monitor the Forum regularly and always respond to posts promptly. I look forward to 'seeing' you on the 3DNA Forum (http://forum.x3dna.org/).
• Post on the Forum to ask any 3DNA-related questions, or share your experience/use-case with the community. Note that even if you've registered, you must post your questions yourself directly on the Forum to get them answered. Specifically, I do not post your questions asked privately via email on the Forum on your behalf.
• Click the Notify button (in the upper right corner) to receive email alert of new posts in the threads or sections you are interested in. I get notified for each and every new post on the Forum so I can react promptly.
• Share what you've learned through help from others. Share what you know that could also be of interest to the general 3DNA user community. Be helpful.
• Behave yourself. No spam or trolling is allowed on the Foum. Violators are removed immediately without any further notice.

2

General discussions (Q&As) / Re: Top view of DNA

« Last post by maryatx3dna on May 18, 2017, 11:38:09 am »

I will check and come back.

I didn't see anything like that in chimera or pdb.
If I just rotate and position it will be biased.


Thanking you
Mary

3

General discussions (Q&As) / Re: Top view of DNA

« Last post by xiangjun on May 18, 2017, 10:58:19 am »

Hi mary,

Thanks for providing further details. Now I understand what you want to achieve. 

Does 3DNA correct the orientation of pdb automatically?

No, 3DNA does correct the orientation of pdb automatically.

The stack2img command is intended to be used with the analyze-generated 'stacking.pdb' file, as shown in the example from stack2img -h. It is not a general purpose grogram to set an arbitrary structure in top view. The DNA image (within x3dna_v1.5.pdf) you attached is a fiber model that is already in top view.

If you can find the helical axis, as in the case of 'dne_l.pdb', you could follow recipe #4 ($X3DNA/R4_4way_junction) described in the the 2008 3DNA Nature Protocols paper. Alternatively, you may find blcoview helpful.

You should also look elsewhere (e.g., PyMOL, Chimera, etc) for such functionality.

Xiang-Jun

4

General discussions (Q&As) / Re: Top view of DNA

« Last post by maryatx3dna on May 18, 2017, 06:51:27 am »

Hi

I am attaching the four files

1. topview_3dna.png   the figure i saw in x3dna tutorial
2.  a dna structure dne_l.pdb
3. topview  dne_l.ps from 3dna  ---> is this figure came out as intended?
4. the modified dna pdb clust1.pdb  ---> i hope its reproducible
5. the figure obtained from 3dna for top view  clust1.ps

Does 3DNA correct the orientation of pdb automatically?


mary

5

General discussions (Q&As) / Re: Top view of DNA

« Last post by xiangjun on May 18, 2017, 06:25:36 am »

Please provide a minimal reproducible example.

Thanks,

Xiang-Jun

6

General discussions (Q&As) / Top view of DNA

« Last post by maryatx3dna on May 18, 2017, 06:13:34 am »

Hi

I want to get the top view and side view of a DNA structure.
I got it from stack2img command.
It works well for a pdb i downloaded from PDB database.

When i do it for a pdb i extracted from my trajectory analysis i get only a side view (not the normal side view). The view i am obtaining for the top view and the side are the same ; the one i could see if i open it in any visualization software. The pdb has modofied residues ; but its ok (since the modification is taken care of) and the pdb works well with findpair and analysis commands.

So what must be the problem ; the top and side view option are not working on my pdb


thanking you

mary

7

General discussions (Q&As) / Re: Definition of gauche and trans for gamma torsion angles

« Last post by xiangjun on May 15, 2017, 03:09:26 pm »

There are two conventions to report torsion angles: [-180, +180] or [0, 360]. As noted clearly in 'analyze' output, 3DNA adopts the former. For conversion to the later, simply add 360 to a negative value from 3DNA.

HTH,

Xiang-Jun

8

General discussions (Q&As) / Definition of gauche and trans for gamma torsion angles

« Last post by lvelve0901 on May 15, 2017, 02:30:20 pm »

Hi Xiangjun,

I have a general question about the definition of gamma torsion angles in 3DNA.

I read some paper about gamma torsion angles and it seems the angular space for the angles are from -360 ~ 360 degree.

For example, in paper titled "Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves" The paper defined

Values of γ angle were classified according to
classical three-fold pattern into: gauche + (60° ± 30°),
trans (180° ± 30°), gauche – (300° ± 30°) conformations.

However, in 3DNA, the angular space of gamma is from -180 --> 180. So I am wondering whether there is any degeneracy in the angular space defined in 3DNA?

Best,
Honglue

9

General discussions (Q&As) / Re: global DNA curvature analysis

« Last post by xiangjun on May 14, 2017, 11:45:55 am »

Does the FAQ item "How to calculate DNA bending angle?" (http://forum.x3dna.org/faqs/how-to-calculate-dna-bending-angle/) help? See also the 2008 3DNA Nature Protocols paper which contains a concrete example with detailed script/datafile on exectly this topic.

HTH,

Xiang-Jun

10

General discussions (Q&As) / global DNA curvature analysis

« Last post by xiaolei on May 14, 2017, 11:25:11 am »

Dear Dr. Lu,
I know you have answered many times in the topic of how to calculate global DNA curvature, as my background is largely biology with almost none computational background, I feel hard to understand when you explain it in a computational or mathematical way about this topic in the forum. I am asking simply that: Is it a way to input a protein/DNA complex structure coordinate (PDB) into w3DNA server or 3DNA program on user's computer and get a global DNA curvature (DNA bending) results, for example such as in protein/DNA complexes papers phrases like "The X-ray structure shows that the DNA is bent overall to 17 􏰆degree",  I'd like to know how to get the overall bent number ( the "17 degree" in my example)  from w3DNA or 3DNA program.

Thanks ahead!