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Author Topic: Jove Questions and Supplimental Files  (Read 5148 times)

Offline acolasanti

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Jove Questions and Supplimental Files
« on: August 09, 2013, 05:11:25 pm »
Please ask general questions about the Jove paper in this section of the forum.  I will set up a topic for each Protocol section, please put questions or comments in the appropriate place for ease of reference. 

Thank you,

Andrew Colasanti

Offline aathithya

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Re: Jove Questions and Supplimental Files
« Reply #1 on: January 25, 2020, 11:56:53 pm »
Sir,
Could you please share the supplementary files for protocol 4? I wanted to know the template file format for .list file containing the list of structures to be analyzed.

Thank you. 

Offline xiangjun

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Re: Jove Questions and Supplimental Files
« Reply #2 on: January 26, 2020, 10:06:14 am »
Hi,

Thanks for your interest in our 2013 3DNA JoVE article. As you noticed, this JoVE section is not complete (unfortunately). Moreover, Andrew Colasanti is no longer involved in the 3DNA project for many years. You may ask Dr. Wilma Olson directly to see if she has the original data files.

Even though I do not have the supplementary files for protocol 4 you requested, you could find an example of the list file by performing the following steps in the $X3DNA/examples/ensemble/md folder. Check the content of file pdb_list.dat.

Code: [Select]
more README
x3dna_ensemble analyze -h
x3dna_ensemble analyze -b bpfile.dat -p 'pdbdir/model_*.pdb' -o ensemble_example3.out
more pdb_list.dat

Best regards,

Xiang-Jun



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

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Offline aathithya

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Re: Jove Questions and Supplimental Files
« Reply #3 on: January 27, 2020, 07:10:31 am »
Thank you sir. It was useful

 

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.