https://wiki.pymol.org/index.php?action=history&feed=atom&title=Nuccyl 2026-05-15T05:00:03Z Revision history for this page on the wiki MediaWiki 1.35.1 https://wiki.pymol.org/index.php?title=Nuccyl&diff=7100&oldid=prev 2014-03-28T02:00:24Z

<p>4 revisions</p> <p><b>New page</b></p><div>See [http://www.biosci.ki.se/groups/ljo/software/nuccyl.html Nuccyl Home]<br /> <br /> ==Overview==<br /> '''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<br /> <br /> [[Image:Phe_trna_small.jpg|thumb|Example Nuccyl Image]]<br /> [[Image:45s_rna_small.jpg|thumb|Example Nuccyl II]]<br /> [[Image:50s_small.jpg|thumb|Example Nuccyl III]]<br /> [[Image:P4p6_small.jpg|thumb|Example Nuccyl IV]]<br /> <br /> 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.<br /> <br /> [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&amp;db=PubMed&amp;list_uids=12824344&amp;dopt=Abstract publication] describing the program is also available.<br /> 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&amp;db=PubMed&amp;list_uids=12930962&amp;dopt=Abstract paper] has also been published.<br /> <br /> ----<br /> The four example images Copyright © 2000-2005 Luca Jovine. Do '''NOT''' reuse them without contacting him or reading his release license for the images!<br /> <br /> [[Category:PyMol_Integration|Nuccyl]]<br /> [[Category:Nucleic_Acids|Nuccyl]]<br /> [[Category:Biochemical_Properties]]</div>

Pyadmin https://wiki.pymol.org/index.php?title=Nuccyl&diff=7097&oldid=prev 2005-08-05T07:57:01Z

<p>Change of the nuccyl URL</p> <p><b>New page</b></p><div>See [http://www.biosci.ki.se/groups/ljo/software/nuccyl.html Nuccyl Home]<br /> <br /> ==Overview==<br /> '''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<br /> <br /> [[Image:Phe_trna_small.jpg|thumb|Example Nuccyl Image]]<br /> [[Image:45s_rna_small.jpg|thumb|Example Nuccyl II]]<br /> [[Image:50s_small.jpg|thumb|Example Nuccyl III]]<br /> [[Image:P4p6_small.jpg|thumb|Example Nuccyl IV]]<br /> <br /> 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.<br /> <br /> [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&amp;db=PubMed&amp;list_uids=12824344&amp;dopt=Abstract publication] describing the program is also available.<br /> 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&amp;db=PubMed&amp;list_uids=12930962&amp;dopt=Abstract paper] has also been published.<br /> <br /> ----<br /> The four example images Copyright © 2000-2005 Luca Jovine. Do '''NOT''' reuse them without contacting him or reading his release license for the images!<br /> <br /> [[Category:PyMol_Integration|Nuccyl]]</div>

Gregori