Re: [support] asking a problem about creating DNA strand

[Ninad Sathaye]

Hi Mingxing,

In NanoEngineer-1, the B-DNA models are the reduced models, called either PAM3 or PAM5 ( IIRC  PAM3 being the default.)

In PAM3 (PseudoAtomModel), 3 pseudo-atoms represent a DNA base-pair.  In order to visualize DNA strands in a PDB file, I think you need a PAM3 -> Atomistic conversion.

I don't seem to remember if we supported pseudoatom to atomistic conversion.  I don't have NE1 installed in my laptop so can't verify this.  Please go to Build->DNA and see if the command toolbar on the top has a button which reads PAM to Atomistic conversion.  You will find options such as PAM3->PAM5 or PAM5->PAM3 on the command toolbar. Perhaps PAM to Atomistic option would sit next to it, if it is supported!

I am copying this message to nanoengi...@googlegroups.com to see if someone can verify this further/ suggest a solution.

Best Regards,
Ninad

2012/1/5 张明星 <starm...@126.com>

Hi,

My name is Mingxing Zhang, a student in Dalian institute of chemical physics (DICP), Chinese Academy of Sciences.
I use Nanoengineer-1 to creat DNA strands,  and export the structure as xxx.pdb file, but when the file is opened by other softwears, there's no detail information (such as bases,phosphate and deoxyribose) of the DNA strand was found. i don't know why could this happen. Could you help me, please? Many thanks for your help.

 

Best wishes for you! Looking forward to your reply!

 

Sincerely,
Mingxing Zhang

--

此致

张明星

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[zhu zhu]

I am facing the same issue!
Are there any current solutions to show more detailed information (especially for the phosphate and deoxyribose) of DNA strands?

Best Regards,

June

[Tom]

Sorry to have to be the one to tell you, but there is no atomistic support for DNA. The best you can do is convert PAM3 to PAM5 with the Convert DNA button which gives you 1 pseudo atom for the base, phosphate and deoxyribose. If I was still modeling DNA origami, I would use SAMSON Connect to do it. It looks like they have a free extension that supports modeling DNA origami https://www.samson-connect.net/element/dda2a078-1ab6-96ba-0d14-ee1717632d7a.html

Best Regards,

Tom

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[zhu zhu]

Hi Tom

Thank you for your kind reply! 

I will check out the SAMSON and give it a try.

Best Regards,

June