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Author Topic: Top view of DNA  (Read 154 times)

Offline maryatx3dna

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Top view of DNA
« 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

Offline xiangjun

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Re: Top view of DNA
« Reply #1 on: May 18, 2017, 06:25:36 am »
Please provide a minimal reproducible example.

Thanks,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline maryatx3dna

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Re: Top view of DNA
« Reply #2 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

Offline xiangjun

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Re: Top view of DNA
« Reply #3 on: May 18, 2017, 10:58:19 am »
Hi mary,

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

Quote
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
« Last Edit: May 18, 2017, 11:42:16 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline maryatx3dna

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Re: Top view of DNA
« Reply #4 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

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.