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Questions and answers => w3DNA -- web interface to 3DNA => Topic started by: jenson on July 25, 2019, 09:48:40 am

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Title: Fiber pdb not loading in Analysis
Post by: jenson on July 25, 2019, 09:48:40 am
Hello,

I was wondering if you could help me solve a problem please.

I have made a fiber B-form DNA with my custom 20 bp sequence using web 3DNA and I am trying to submit the pdb that web3DNA has generated, back into the Analysis page. I want to use this to compare the data with my protein-DNA structure to see any conformation changes.

Unfortunately, when I upload the generated fiber DNA pdb into the Analysis page,  it keeps saying:
'ERROR: The upload file has NO ATOM or Standard base. Please submit another one.'

I have not changed anything in the pdb, it is the same file as was generated by web3DNA 2.0.

Do you have any suggestions?

Thank you for any help you can give with this matter - it is most appreciated.
Title: Re: Fiber pdb not loading in Analysis
Post by: shuxiang on July 25, 2019, 09:57:43 am
Thank you for using web 3DNA 2.0. I used the B-fiber model to generate a structure (see attachment) and analyze it with the Analysis module. It works. It will be very helpful if you can attach or paste the content of your pdb file?
Title: Re: Fiber pdb not loading in Analysis
Post by: jenson on July 25, 2019, 10:04:00 am
Thanks for your reply.

I have downloaded your attached fiber model and then uploaded into the analysis and it still says the same problem. Please see attached.
Title: Re: Fiber pdb not loading in Analysis
Post by: jenson on July 25, 2019, 10:05:23 am
I have attached my pdb file here too.

Thank you.
Title: Re: Fiber pdb not loading in Analysis
Post by: shuxiang on July 25, 2019, 10:28:23 am
I have found the reason ;D.  Just change your file name to something like "fiber_model_1.pdb" without parentheses in the filename. It is a bug and I will fix it.
Title: Re: Fiber pdb not loading in Analysis
Post by: jenson on July 25, 2019, 10:51:40 am
Thank you - this works now!

Thanks very much for your help :)

kind regards
Title: Re: Fiber pdb not loading in Analysis
Post by: shuxiang on July 25, 2019, 10:57:17 am
I have fixed the bug and you can use your original file name. Thank you for finding this bug. :)
Title: Re: Fiber pdb not loading in Analysis
Post by: xiangjun on July 25, 2019, 11:10:00 am
Hi Shuxiang,

Based on this use-case, I thought it helps to add a link that directs a fiber model to the 'Analysis' module. Currently, the 'Fiber' module has a link: [Use this structure for mutation]. The new link could be: [Use this structure for analysis]. What do you think?

Best regards,

Xiang-Jun
Title: Re: Fiber pdb not loading in Analysis
Post by: jenson on July 25, 2019, 11:15:01 am
Thank you for fixing this  :D
Title: Re: Fiber pdb not loading in Analysis
Post by: shuxiang on July 25, 2019, 11:22:27 am
Good idea. I will work on this feature when I finish the code for RNA analysis today. :)

Hi Shuxiang,

Based on this use-case, I thought it helps to add a link that directs a fiber model to the 'Analysis' module. Currently, the 'Fiber' module has a link: [Use this structure for mutation]. The new link could be: [Use this structure for analysis]. What do you think?

Best regards,

Xiang-Jun

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.