How to build a single-stranded RNA structure of arbitrary sequence?

[xiangjun]

As of v2.1, the fiber utility has several new options that make building single-stranded RNA structures of arbitrary sequence a snap:

• -s for single-strand
• -r for RNA structure
• -seq for specifying arbitrary sequence directly on the command line

For example, to generate a single-stranded RNA structure of sequence 'AUUGGUUC', do the following:

Code: [Select]

fiber -s -r -seq=AUUGGUUC ss-RNA.pdb
# the -s and -r options can be combined as -sr or -rs
fiber -sr -seq=AUUGGUUC ss-RNA.pdb
Technically, the RNA model is based on A-DNA model (#1 in the list), with the O2' atom attached on the sugar, and T replaced by U. The -s option simply extracts the leading strand from the default duplex.