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Author Topic: Fiber pdb not loading in Analysis  (Read 41048 times)

Offline jenson

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Fiber pdb not loading in Analysis
« 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.
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Offline shuxiang

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Re: Fiber pdb not loading in Analysis
« Reply #1 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?
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Offline jenson

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Re: Fiber pdb not loading in Analysis
« Reply #2 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.
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Offline jenson

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Re: Fiber pdb not loading in Analysis
« Reply #3 on: July 25, 2019, 10:05:23 am »
I have attached my pdb file here too.

Thank you.
« Last Edit: July 25, 2019, 11:13:01 am by jenson »
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Offline shuxiang

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Re: Fiber pdb not loading in Analysis
« Reply #4 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.
« Last Edit: July 25, 2019, 10:56:34 am by shuxiang »
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Offline jenson

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Re: Fiber pdb not loading in Analysis
« Reply #5 on: July 25, 2019, 10:51:40 am »
Thank you - this works now!

Thanks very much for your help :)

kind regards
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Offline shuxiang

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Re: Fiber pdb not loading in Analysis
« Reply #6 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. :)
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Offline xiangjun

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Re: Fiber pdb not loading in Analysis
« Reply #7 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
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Offline jenson

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Re: Fiber pdb not loading in Analysis
« Reply #8 on: July 25, 2019, 11:15:01 am »
Thank you for fixing this  :D
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Offline shuxiang

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Re: Fiber pdb not loading in Analysis
« Reply #9 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. :)

Quote from: 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
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Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University