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Messages - Damien

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1
w3DNA -- web interface to 3DNA / Re: Structural quality
« on: January 11, 2013, 12:36:11 pm »
Thanks for the reply Xiang-Jun! I'm going to test the structure with MolProbity.

This DNA is in fact 1BNA prologated with a model DNA and made cyclized.

Thanks for your help!

Damien

2
w3DNA -- web interface to 3DNA / Structural quality
« on: January 11, 2013, 12:00:39 pm »
Dear Xiang-Jun,

Could you look at the attached cyclized DNA structure and give your opinion about its structural quality by using Web 3DNA? It seems that many covalent bond angles like for example N1-C2-O2 or C3'-C4'-C5' are not correct. Do you confirm?

Many thanks

Damien

3
w3DNA -- web interface to 3DNA / Re: misshapen base ring
« on: January 07, 2013, 02:13:38 pm »
Many thanks for your help Xiang-Jun! I appreciate.

Damien

4
w3DNA -- web interface to 3DNA / Re: misshapen base ring
« on: January 07, 2013, 12:43:07 pm »
Many thanks Xiang-Jun for this reply!

No, I did not suggest to change anything in 3DNA. I'm just looking for a way to avoid the visual inspection of the bases one by one.

I have the answer to my question in your reply: Web 3DNA does not recognize these distorted bases. This explains why the analysis in Web 3DNA results in 277 bp and not 280 (it seems however  that one "bad" base is recognized, DT 8 F).

So, 277 instead of 280 is the indication that something goes wrong. Then, a look at the RMSD in parentheses from the Nucleic acid structural parameter summary file is also a relevant parameter.

Am I right?

Thanks

Damien

ps: the goal of all this is to repair only the distorted base rings (as minimization on such a long structure can be very very long)

5
w3DNA -- web interface to 3DNA / Re: misshapen base ring
« on: January 07, 2013, 11:12:21 am »
Hi Xiang-Jun,

Here is the 280 bp circular structure. Bases 275 and 276 of chain E, and 7 and 8 of chain F pose problem.

Thanks

Damien

6
w3DNA -- web interface to 3DNA / misshapen base ring
« on: January 07, 2013, 10:25:54 am »
Dear all,

I have a long DNA 3D structure that contains 4 bases with misshapen rings. I detected them thanks to visual inspection.

How can I identify these structural deficiencies in a more automatic manner with Web 3DNA? From the list of numbers resulting from "Analysis", can I detect these misshapen bases?

Thanks for your help,

Damien

7
Many thanks Xiang-Jun for your help! I appreciate!

Damien

8
Many many thanks Xiang-Jun for this prompt reply! I appreciate!

OK, I understand the approximation for the sugar-phosphate backbone.

I have two questions:

- The default O3'-P distance is 4.5A. From the ADIT server of the PDB, the expected value is 1.6A. What is in fact the range of the possible values?

- Could you indicate some tools alllowing to do energy minimization?

Thanks again,

Damien

9
Dear Xiangjun,

I analyzed the DNA molecule contained in PDB 2AOR from Web 3DNA. I then downloaded the parameter file. And I performed a reconstruction from the parameter file.

The resulting structure build.pdb contains many O3'-P bonds having a too long length, up to 4 A.

May you tell me what I made wrong ?

Many thanks for your help

Damien

10
General discussions (Q&As) / Re: Rebuild DNA from C trace
« on: April 21, 2011, 04:57:17 am »
Hi Xiang-Jun,

Commercial Yasara can perform the rebuild but it is not straightforward. I have not received the protocol yet but it needed to write a script, so to be quite quite familiar with it.

I strongly think that a rebuilding tool in 3DNA would be very useful.

Damien

11
General discussions (Q&As) / Re: Rebuild DNA from C trace
« on: April 20, 2011, 03:13:49 am »
Hi Xiang-Jun

Many thanks for your answer.

One of my colleague just sent me the whole structure rebuilt from the C-trace I provided. He used Yasara. I do not still know how he did, I should receive the modeling protocol today.

Just a word of context:

I use 3D app like 3DS Max or Blender to add a straight DNA portion to macromolecular complexes made of several proteins. The DNA is deformed to bind to the known binding sites. I only use the C-trace because it reduces the number of atoms and allows real-time deformation. When I have the protein complex with the DNA, I can export in the PDB format, the PDB file containing the protein coordinates but only the trace of DNA C-atoms. Then, with the whole rebuilt DNA, it is possible to refine the structure using approaches like MD.

Damien

12
General discussions (Q&As) / Rebuild DNA from C trace
« on: April 15, 2011, 03:16:49 am »
Dear Xiang-Jun,

I have a PDB file of a DNA portion. It only contains the carbon trace (the C4 atoms). I would like to know whether it is possible to rebuild the whole structure from this trace with 3DNA? If not, do you know a way to do so?

Many thanks for your help

Damien

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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.