Editing Nuccyl (section)

==Overview==
'''nuccyl''' is a [http://www.perl.org/ Perl] program that allows [http://www.pymol.org/ PyMOL], a powerful open-source molecular modeling system, to display atomic models of nucleic acids in a highly simplified representation. By depicting the nucleic acid backbone as a cartoon and the bases of nucleotides as cylinders, similarly to the excellent programs [http://sgce.cbse.uab.edu/ribbons/ Ribbons] and [http://www-ibmc.u-strasbg.fr/upr9002/westhof/download.html Drawna], nuccyl and PyMOL allow to quickly grasp the overall folding of an RNA or DNA molecule

[[Image:Phe_trna_small.jpg|thumb|Example Nuccyl Image]]
[[Image:45s_rna_small.jpg|thumb|Example Nuccyl II]]
[[Image:50s_small.jpg|thumb|Example Nuccyl III]]
[[Image:P4p6_small.jpg|thumb|Example Nuccyl IV]]

nuccyl produces base cylinder coordinates and command files to display them with PyMOL. The base pair analysis programs [http://beta-ndb.rutgers.edu/services/download/index.html#rnaview RNAView] and [http://rutchem.rutgers.edu/%7exiangjun/3DNA/ 3DNA] can also be optionally used to obtain starting input files for nuccyl.

[http://beta-ndb.rutgers.edu/services/download/index.html#rnaview RNAView] can be downloaded and installed as [http://ndbserver.rutgers.edu/services/help/rnaview-readme.html described]; a [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12824344&dopt=Abstract publication] describing the program is also available.
Information and download links for [http://rutchem.rutgers.edu/%7exiangjun/3DNA/ 3DNA] may be found at the program's [http://rutchem.rutgers.edu/%7exiangjun/3DNA/ home page]; a [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12930962&dopt=Abstract paper] has also been published.

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The four example images Copyright © 2000-2005 Luca Jovine.  Do '''NOT''' reuse them without contacting him or reading his release license for the images!

[[Category:PyMol_Integration|Nuccyl]]
[[Category:Nucleic_Acids|Nuccyl]]
[[Category:Biochemical_Properties]]