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1
RNA structures (DSSR) / Re: Water H-Bonding with surrounding residues
« Last post by xiangjun on Today at 10:26:30 am »
Hi,

Thanks for posting on the 3DNA Forum!

Could you elaborate on what you want to achieve specifically? Please use a concrete example so that I (and others) can better understand you.

Best regards,

Xiang-Jun


2
RNA structures (DSSR) / Water H-Bonding with surrounding residues
« Last post by kanavkalra on Today at 09:36:50 am »
Dear Dr. Xiang-Jun Lu,
May I know if there exists any option that could help me get data for the Water H-Bonding with the surrounding residues?

Regards,
Kanav Kalra
3
Thank you for the explanation. 
4
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
5
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.

6
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
7
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   
8
It works. Thank you so much. :)
9
Hi Shuxiang,

The '&' symbol in DSSR-derived dot-bracket-notation (DBN) is a convention between DSSR and VARNA to signify different chains or breaks between different segments of the same chain. Other 2D viewers may not recognize it, as is the case for FORNA.

You could use the --dbn-break=no option to remove them, as documented in the DSSR manual (Section 3.16.12, shown below).

3.16.12 The --dbn-break option

By default, DSSR employs the symbol ‘&’ to separate multiple chains or
chain breaks in dbn, for compatibility with VARNA. By using
--dbn-break, one can choose any of the characters in the string
“&.:,|+”. For example, by running the following command on the
Dickerson DNA dodecamer [16] structure 355d, one would get a
whole-structure dbn composed of those from the two chains
connected by ‘+’:

------------------------------------------------------------
x3dna-dssr --dbn-break=+ -i=355d.pdb

>355d nts=24 [whole]
CGCGAATTCGCG+CGCGAATTCGCG
((((((((((((+))))))))))))
------------------------------------------------------------

With --dbn-break=no, no symbol will be used to separate different
chains or intra-chain breaks: for 355d, the dbn would be
(((((((((((()))))))))))).

HTH,

Xiang-Jun
10
RNA structures (DSSR) / How to display RNA secondary structure with & in forna?
« Last post by shuxiang on May 15, 2018, 11:10:38 am »
Dear Xiangjun,

I tried to use the following dbn file generated by DSSR and display its RNA secondary structure in forna (a RNA secondary structure visualization tool). However, it looks like forna doesn't recognize multiple sequences and "&" notation. It there a way to get around this? Thank you.

>2F4V nts=1511 [2F4V] -- secondary structure derived by DSSR
UGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGG&CCGCGGGGUUUU&ACUCCG&UGGUC&AGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUU&GCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAA&CCCGGGACGAAACCCCCGACGA&GGGGACUGACGGUACCGGG&GUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCU&CCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGG&AGCCUACGGG&CAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUC&A&UUCU
....((((..[.[[[..)))).((((.(((((..(((((((((....(((.(((..(((..((.((&((((((((....&.)))))&)))))&.)))))......(((......((((((((..((...(((((((.(((((....((((((....)))))).....)))))....((((.(((((....))))).))))...((((...&)))).)))))))..))))))))))(((....(((..((((((((.......)))))))))))......)))..((((((((....))))...))))))).(((((............))))).((((....))))...)))))).).....(.(((...((.((....)).).))))).)).))))))..((((.......(((....)))......))))....&(.(((...(....((((.....&)))).....)....))).)&......((((([[[...(((((.....((.]]])).......))))))))))..)))))))))..........((([[...(.((((...(((.(((((((.((((((((((......((((((.....))))))....))))))))..)))))))))..(((.(((((...((((((((...(((((((....((........)).......)))))))...).......((....)).)))))))..)))))..))..))))...))))....((((((...((...((((.........))))...))))))))......{...((((((..((((((((((...&))))))))))...((..]])).....)))))))))).(((......((((....))))....)))...]]].](((((.(((((((.((..(((((..((((((((((......((........))..........((((((...(...((............(.(....).)........(((....).))........))).((.(((...((((((.(....(((((((((....)))..((((......))))..)))))).....((((.(((((.....(....(.......)..)......)))))..(..(((((....))))).....)..)))).....).).)))...)).))))).....))))))..[)).)))))))).(...(((((((.....(((..((..((((....))))..))....))).....)))))))......(....(((((((........)))))))....)..)..))))).....(((((((......]...)))))))......))...)))))))))).))..(.(..((.(.((((.(((..((.(((.((((((...(.((((...&.(((....))&).)))).)..)))))).))).))..))).))))..).))...)..)..(((((((((....)))))))))}....&.&....

Best,
Shuxiang                                                           

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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.