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Questions and answers => RNA structures (DSSR) => Topic started by: shuxiang on May 17, 2018, 11:31:00 am

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Title: DSSR-enhanced visualization web server cannot display ribosome structures?
Post by: shuxiang on May 17, 2018, 11:31:00 am

Dear Xiangjun,

I used DSSR-enhanced visualization web server to display ribosome structures such as 5afi, 5j4b. All my tried failed. I'm not sure it is my browser problem or the web server inner error. Thank you.

Best,
Shuxiang   

Title: Re: DSSR-enhanced visualization web server cannot display ribosome structures?
Post by: xiangjun on May 17, 2018, 11:47:56 am

Hi Shuxiang,

The ribosome structures 5afi and 5j4b are huge. In CIF format, they are 26M and 37M respectively, which exceed the 18M size limit. See the DSSR-Jmol paper. The relevant section is shown below.

Quote

DSSR web service

The web service is hosted at Columbia University, via a single-file PHP script that calls the DSSR command-line tool for back-end analysis. The DSSR web service runs independently of Jmol, and accepts atomic coordinates in mmCIF or PDB format. The service also takes a four-letter PDB id to automatically fetch the corresponding mmCIF formatted coordinate file from the RCSB PDB (20) (see the Supplementary Data). For an NMR ensemble, only the first model is analyzed by default. For X-ray crystal structures, the asymmetric unit is analyzed. The DSSR algorithm works for both DNA and RNA, either in isolation or in their complexes with proteins. The server has an 18MB-size limit for uploaded coordinate files. For DNA/RNA structures with <300 nucleotides, it takes DSSR less than one second to run (see Table 1 of reference (9)).

So what you observed is as expected. It is a documented limitation of the DSSR-Jmol website.

Xiang-Jun

Title: Re: DSSR-enhanced visualization web server cannot display ribosome structures?
Post by: shuxiang on May 17, 2018, 12:08:56 pm

Thank you so much for your quick response. Just now I did a test and found a interesting thing.
I uploaded the 5afi.cif file (26MB) to the web server from a local machine, it works.
I fetched 5afi ID directly in the web server, it failed.

Title: Re: DSSR-enhanced visualization web server cannot display ribosome structures?
Post by: xiangjun on May 17, 2018, 12:37:20 pm

Interesting observation. When you upload a structure from your local machine, it is first parsed by Jmol. The coordinates (which are smaller than the initial .cif file) are then passed to DSSR on the server. That explains your test case of 5afi.

Overall, the simple interactive DSSR-Jmol website is not designed to handle those large ribosomal structures.

Xiang-Jun

Title: Re: DSSR-enhanced visualization web server cannot display ribosome structures?
Post by: shuxiang on May 17, 2018, 12:58:25 pm

Thank you for the explanation. 

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