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Questions and answers => RNA structures (DSSR) => Topic started by: shuxiang on February 11, 2019, 10:24:32 am

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Title: no nucleotide in some structures
Post by: shuxiang on February 11, 2019, 10:24:32 am

Hi Xiang-Jun,

I'm using DSSR to analyze some structures and it showed there is no nucleotide was found. When I visualized these structures using pymol. I indeed saw nucleotides are there. For example (6CEV):

x3dna-dssr -i=6cev.pdb

Thanks. :)

Best,
Shuxiang

Title: Re: no nucleotide in some structures
Post by: xiangjun on February 11, 2019, 11:07:43 am

By default, DSSR checked for ATOM/HETATM records with the alternative location (altloc) set either as space (most common) or 'A'. In PDB entry 6CEV, the DNA atoms have altloc as 'B'. That's why you do not see any results from a default DSSR run.

Try: x3dna-dssr -i=6cev.pdb --altloc=B

Best regards,

Xiang-Jun

Title: Re: no nucleotide in some structures
Post by: shuxiang on February 11, 2019, 11:41:21 am

Thank you so much for the explanation and an option to solve my problem.

Best,
Shuxiang

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