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Author Topic: Adding a modified or non standard bases in a default library  (Read 163 times)

Offline tanashree

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Adding a modified or non standard bases in a default library
« on: November 19, 2019, 12:09:14 pm »
I want to analyze the base-pair parameters of 13 mer DNA double helix. I have one modified base Thymine Glycol in my strand.

I added the name in baselist.dat I am using 2.0 version.  Also, I kept the Atomic_TG.PDB file in config folder as shown for 5MC modification.  When I tried to analyze program is analyzing just for the 10 base pairs and not all 13.

I am attaching DNA duplex file and separate modified base file and also the .dat file in config folder

Thanks & Regards,
Tanashreee

Offline xiangjun

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Re: Adding a modified or non standard bases in a default library
« Reply #1 on: November 19, 2019, 01:17:08 pm »
Hi Tanashreee,

Thanks for using 3DNA and for posting your questions on the Forum.

Quote
I added the name in baselist.dat I am using 2.0 version.  Also, I kept the Atomic_TG.PDB file in config folder as shown for 5MC modification.  When I tried to analyze program is analyzing just for the 10 base pairs and not all 13.

Please upgrade to 3DNA v2.4, which detects 12 base-pairs out of the expected 13. Version 2.0 is more than 10 years old, and there is no practical reasons to use it anymore.

3DNA does not detect the ADE-TG pair due to improper labeling of base atoms in the modified TG. See the attached image of the pair, and pay close attention to the TG base ring (e.g., C7 connects to N1 etc.)

Rectify names of the TG base atoms following PDB convention (as for T), 3DNA should then work. Please have a try and report back how it goes.

Best regards,

Xiang-Jun




« Last Edit: November 19, 2019, 03:40:55 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline tsjbioinfo

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Re: Adding a modified or non standard bases in a default library
« Reply #2 on: November 20, 2019, 08:45:56 am »
Thanks, Prof. xiangjun for your prompt reply. I tried with the changes you suggested and it worked. The modified base was considered as t. Now another doubt is I have to run these calculations for multiple PDB files at a time. I guess analyze option is overwriting the file names wehn I am trying to run in for loop and I could not find any option to give the output file name after analyze command. 

Thanks,
Tanashree

Offline xiangjun

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Re: Adding a modified or non standard bases in a default library
« Reply #3 on: November 20, 2019, 11:10:04 am »
Quote
I tried with the changes you suggested and it worked.

Glad to hear that the suggested method works. Thanks for the update.

Quote
Now another doubt is I have to run these calculations for multiple PDB files at a time. I guess analyze option is overwriting the file names wehn I am trying to run in for loop and I could not find any option to give the output file name after analyze command.

Since you are running 'analyze' in a loop to process multiple PDB files, you should be able to rename the default output file as desired. Without further details, that's all I could say.

Best regards,

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

Offline tsjbioinfo

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Re: Adding a modified or non standard bases in a default library
« Reply #4 on: November 20, 2019, 11:58:38 am »
Dear Prof. xiangjun, thanks for your suggestion. It worked with do_x3dna VMD plugin.

Thanks,
Tanashree

Offline xiangjun

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Re: Adding a modified or non standard bases in a default library
« Reply #5 on: November 20, 2019, 12:05:58 pm »
Quote
It worked with do_x3dna VMD plugin.

I do not know if it works now. For any do_x3dna specific questions, please ask the authors/developers directly. I was not involved in that project and I cannot provide any practical help for do_x3dna.

Best regards,

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

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.