Information

[Ijaz rksad]

Hello,

Respected all i am trying to insert DNA strand how i can insert in nanoengineer 1.

Thank you

[Tom]

Here is a video that shows how to do it in NE1. https://youtu.be/_sB97_F4Vh4

NE1 doesn't use a full atom model. It has a pseudo atom 3 or5 model. You can drag the ends of the models to their same color of a different strand to connect them. Though depending on the version of NE1 you have, you cannot assign basepair types. An updated solution would be to:

1. Get the SAMSON Connect, just the free version is fine for now: https://www.samson-connect.net/pricing:

2 Then get their free DNA modeling extension: https://www.samson-connect.net/extensions/dda2a078-1ab6-96ba-0d14-ee1717632d7a

Best Regards,

Tom

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[Ijaz rksad]

Dear Top,
Thank you this video is very helpful for me, now here I have a question that how I can connect how strands because I don't see any option in my software. Please guide me about this issue.
Thank you

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[Ijaz rksad]

Dear professor,
Please guide me here is image but in my icons I did not saw any option for nucleotides to select for collection and how to connect.

Thank you. 

[Tom]

Here is how you connect the strands: https://youtu.be/7c61CPvGkr8

I don't know what version of NE1 that is. This is one way to assign basepairs. https://youtu.be/bTq2NzIOaWc

 You might be able to upload a text file after clicking on the origami icon.

NE1 is not going to be a good solution for you in working with DNA. I still recommend you try the following:

1. Get the SAMSON Connect, just the free version is fine for now: https://www.samson-connect.net/pricing:

2 Then get their free DNA modeling extension: https://www.samson-connect.net/extensions/dda2a078-1ab6-96ba-0d14-ee1717632d7a

Best Regards,

Tom

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[Ijaz rksad]

Dear sir,
I am using Nano engineer-1, version v1.1.1.12.exe.

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[Ijaz rksad]

Dear all,
I have installed nano engineer 1 0.91 (alph9) version but how I did not found to select and connect to strand. Please share any version where all features can be found.
Thank you

[Ijaz rksad]

Dear Dr Tom,
Please send me that version download link which is in your video. That version is awesome.
Thank you

[Tom]

NE1 will prevent you from connecting strands that don't bond together, i.e. 5' end (five-prime end) of one nucleotide connects to the 3' end (three-prime end) of the next nucleotide. You can only connect strand ends with arrows to ends with balls like in this video https://www.youtube.com/watch?v=7c61CPvGkr8

Here is a link to download the version for Windows I use: https://drive.google.com/file/d/1qocfsi84H_fXhns-cZsYsd667ldM1Zhf/view?usp=sharing

Longterm you are going to want to use the free version of SAMSON, and if you post your questions to their forum, you will likely get more help than we can offer here.

Good luck!

Tom

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[Ijaz rksad]

Sir I also try that but here is also problem how to select two nucleotides that are to be connect. And after connecting when I am selecting to change strand colors did not changed. Please sir send that version download link which you have installed in your video.
Thank you

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[Tom]

I don't know what the issue is. When I connect two strands together, they change color as in the attached images. Here is a video on selecting nucleiotides > hold the shift key and the left mouse button.

https://youtu.be/ZhW75dZmh5w  I doubt NE1 is fit to use for any DNA science. There are much better tools available and getting you to switch to SAMSON or something else is better for you

Tom

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[Ijaz rksad]

Dr. Tom,
sir thank you. Help help me a lot once again thank you.

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[Ijaz rksad]

Dear all I have designed structure in Nano engineer 1 but I am confused how I can add sequence. Please guide me.
Thank you all

[Tom]

With the version you downloaded from me, 1.1.14, this is the only way you can do it: https://youtu.be/bTq2NzIOaWc

If you go Help > About NanoEngineer-1 on the first version you had before you downloaded, and it says "NanoEngineer-1.1.1" you use the sequence editor which is somewhere in the DNA menus. I forget where. It seems version 1.1.1 does have the sequence editor and version 1.1.1.14 does not have the sequence editor. You could also possibly write a script that reads in the mmp text file and assigns the base pairs based on the data stored in it, but that would take some work.

Tom

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[Ijaz rksad]

Dear Dr. Tom,
Thank you for your reply and I am asking for that how I can run simulation please if you have youtube videos please share with me I shall be very grateful to you.
Thank you

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[Tom]

The mechanics of doing that in NE1 are like this: https://youtu.be/ITrS7JsQ0Yc

However there is no guarantee that what NE1 is doing with your model is reflecting reality, just so you know.

Tom

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[Ijaz rksad]

Dr. Tom,
Thank you sir.

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