159 lines
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HTML
159 lines
14 KiB
HTML
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<body background="images/bckgrnd.gif" bgcolor="white" link="#003399" alink="#003399" vlink="#003399" text="black">
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<table border="0" cellpadding="0" cellspacing="0" width="617" align="left">
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<tr height="176">
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<td height="176" colspan="2" align="left" valign="top"><img height="12" width="8" src="images/dotclear.gif"><img height="171" width="173" src="images/logo.gif" alt="NCBI Logo"></td>
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<td height="176" valign="top" width="8" align="left"></td>
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<td width="420" height="176" valign="top"><img height="80" width="364" src="images/msthd1.gif" border="0" alt="NCBI News" usemap="#E"><map name="E"><area href="http://www.ncbi.nlm.nih.gov/About/newsletter.html" coords="3,12,356,65" shape="rect" title="NCBI News"></map><br>
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<img height="80" width="340" src="images/msthd1a.gif" border="0" alt="National Center for Biotechnology Information" usemap="#NCBI"><map name="NCBI"><area href="http://www.nih.gov" coords="0,63,133,77" shape="rect"><area href="http://www.nlm.nih.gov" coords="0,41,138,53" shape="rect"><area href="http://www.ncbi.nlm.nih.gov" coords="0,14,248,26" shape="rect"></map><img height="80" width="80" src="images/spring2000.gif" alt="Spring 2000"></td>
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</tr>
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<tr>
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<td width="12" align="left" valign="top"><img height="1" width="1" src="images/dotclear.gif"></td>
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<td width="178" align="left" valign="top"><font size="2" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><br>
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<br>
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<img height="33" width="178" src="images/issue.gif" alt="In this issue"><br>
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<br>
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</font><font size="2" color="black" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>Dazzling Graphics<br>
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with Cn3D 3.0</b></font>
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<p><a href="blast.html"><font size="2" color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>BLAST Offers<br>
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Taxonomic Views</b></font></a></p>
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<p><a href="homologene.html"><font size="2" color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>HomoloGene:<br>
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Clusters of Clusters</b></font></a></p>
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<p><a href="briefs.html"><font size="2" color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>News Briefs</b></font></a></p>
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<p><a href="fly.html"><font size="2" color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>Fly Genome Deposited<br>
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in GenBank</b></font></a></p>
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<p><a href="drosophila.html"><font size="2" color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>Drosophila Finds<br>
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New Home Page</b></font></a></p>
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<p><a href="pubs.html"><font size="2" color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>Recent Publications</b></font></a></p>
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<p><a href="faq.html"><font size="2" color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>Frequently Asked<br>
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Questions</b></font></a></p>
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<p><a href="blastlab.html"><font size="2" color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>BLASTLab</b></font></a></p>
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<p><a href="masthead.html"><font size="2" color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>Masthead</b></font></a></td>
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<td width="8" align="left" valign="top"><img height="1" width="1" src="images/dotclear.gif"></td>
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<td width="420"><br>
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<br>
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<font color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular"><b>Dazzling Graphics with Cn3D 3.0</b></font>
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<p><font color="black" face="Times New Roman,Georgia,Times">The newly released Cn3D 3.0 provides dazzling graphics through the use of the OpenGL graphics library. Coupled with the graphics enhancements are several new rendering options and color schemes. The Cn3D sequence window has also been refined to allow easier selection of residues, and better depiction of secondary structural elements, protein domains, and hetero-atoms alongside the sequence</font><font face="Times New Roman,Georgia,Times">.<br>
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</font> </p>
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<p><font color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular" size="2"><b>Greater Graphics</b></font></p>
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<p><font color="black" face="Times New Roman,Georgia,Times">Cn3D 3.0 depicts solid objects more realistically, taking advantage of highlighting and shadowing. New rendering options include an alpha-carbon backbone </font><font face="Times New Roman,Georgia,Times">“</font><font color="black" face="Times New Roman,Georgia,Times">worm</font><font face="Times New Roman,Georgia,Times">”</font><font color="black" face="Times New Roman,Georgia,Times">, or </font><font face="Times New Roman,Georgia,Times">“</font><font color="black" face="Times New Roman,Georgia,Times">coil</font><font face="Times New Roman,Georgia,Times">”</font><font color="black" face="Times New Roman,Georgia,Times"> representation at three thickness levels. Alpha-helices may now be represented either as blunt-ended cylinders or cylinders with carboxy-terminal </font><font face="Times New Roman,Georgia,Times">“</font><font color="black" face="Times New Roman,Georgia,Times">caps</font><font face="Times New Roman,Georgia,Times">”</font><font color="black" face="Times New Roman,Georgia,Times"> to indicate the direction of the peptide chain. In addition, ions are depicted as translucent spheres. A new color scheme called Sequence Conservation offers several coloring options when multiple sequences are displayed in the sequence window.<br>
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<br>
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This graphical power can be adjusted to allow for differences in computer speeds, video resolutions, or molecule size using a new Cn3D Quality control tab found under View/Drawing settings. Lower resolutions can be used to facilitate faster rotation speeds for larger molecules. Higher resolutions can be chosen when publication-quality figures are desired.</font><font face="Times New Roman,Georgia,Times"><br>
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</font> </p>
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<p><font color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular" size="2"><b>Enhanced Functionality in the Sequence Window</b></font></p>
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<p><font color="black" face="Times New Roman,Georgia,Times">The Cn3D Sequence window operates in either a single or multiple sequence mode. If a single sequence is displayed, then the window is entitled OneD-Viewer and uses a set of options suitable for operations on a single sequence. If more than one sequence is displayed, the window is entitled DDV (DeuxD-Viewer) and a set of options suitable for multiple sequences is active. Columns of a multiple alignment may be colored according to sequence conservation, for example, with these colors mapped to both the sequence and structure windows.</font><font face="Times New Roman,Georgia,Times"><br>
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</font> </p>
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<p><font color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular" size="2"><b>OneD-Viewer Operation</b></font></p>
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<p><font color="black" face="Times New Roman,Georgia,Times">The Sequence window has been given several new abilities in version 3.0. Secondary structural elements are now represented as 3-D-like cartoon images beneath the sequence. NCBI-assigned protein domains are indicated using solid 2-D arrows. Hetero-atoms in the features list are indicated in the sequence display as small triangles positioned near the residues that are closest to them in the 3-D structure. As in earlier versions of Cn3D, additional sequences may be aligned to a structurally anchored sequence by importing FASTA-formatted files or by downloading directly from Entrez over the network.</font><font face="Times New Roman,Georgia,Times"><br>
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</font> </p>
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<p><font color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular" size="2"><b>DDV Viewer Operation<br>
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</b></font></p>
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<p><font color="black" face="Times New Roman,Georgia,Times">When a sequence alignment is shown in the Sequence window, a different set of options is available. The mouse mode may be changed, using the Options menu, from the default of Select to Query in order to use the mouse to identify residue numbers. A Styles panel, also invoked from the Options menu, allows several sequence-alignment display parameters to be adjusted. These include the use of color and the placement of ruler lines.</font><font color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular" size="2"><br>
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</font></p>
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<p><font color="black" face="Times New Roman,Georgia,Times"><img height="496" width="420" src="images/1pah1_small.gif" alt="Figure 1"><br>
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<br>
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</font><font color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular" size="2"><b>Figure 1</b></font><font face="Times New Roman,Georgia,Times" color="#003399" size="2"><b>: </b></font><font face="Times New Roman,Georgia,Times" color="#003399" size="2">Cn3D Structure window view of human phenylalanine hydroxylase (PDB code 1PAH).<br>
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</font></p>
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<p><font color="black" face="Times New Roman,Georgia,Times">The enhanced graphical capabilities of Cn3D 3.0 are illustrated in the views of Human Phenylalanine Hydroxylase (PDB code 1PAH) in Figures 1 and 2. The structure window shows an image of the protein in which the NCBI-defined secondary structural elements, helices and strands, are represented as solid cylinders and planks, respectively, with the pointed ends indicating the amino- to carboxy-terminal direction. An iron atom is seen in the center of the structure, represented as a translucent sphere. Using the Annotation panel, the sites of documented mutations, as taken from Online Mendelian Inheritance in Man (OMIM), are marked by showing these amino acid side-chains in a </font><font face="Times New Roman,Georgia,Times">“</font><font color="black" face="Times New Roman,Georgia,Times">fat-tube</font><font face="Times New Roman,Georgia,Times">”</font><font color="black" face="Times New Roman,Georgia,Times"> representation.<br>
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</font></p>
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<center>
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<p><a href="#" csclick="B589065E5" onclick="CSAction(new Array(/*CMP*/'B589065E5'));return CSClickReturn();"><font color="black" face="Times New Roman,Georgia,Times"><img height="200" width="420" src="images/1pah2_small.gif" border="0" alt="Figure 2"><br>
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</font></a><font face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular" color="black" size="1">Click on figure to view enlarged version</font><font color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular" size="2"><b><br>
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</b></font></p>
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</center>
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<p><font color="#003399" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular" size="2"><b>Figure 2</b></font><b><font face="Times New Roman,Georgia,Times" color="#003399" size="2">:</font></b><font face="Times New Roman,Georgia,Times" color="#003399" size="2"> Cn3D Sequence window view of human phenylalanine hydroxylase (PDB code 1PAH).</font></p>
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<div align="left">
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<p><font color="black" face="Times New Roman,Georgia,Times">The accompanying Sequence window shows these mutable residues in a dark shade (red). Secondary structural elements are shown below the sequence. The single NCBI-derived protein domain for this structure is indicated by the arrow that runs from residue 59 to residue 291. Residues proximal to the iron atom in the structure are marked with an H under the sequence.<br>
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<br>
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For more information, navigate to </font><a href="http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.html"><font color="#003399" face="Times New Roman,Georgia,Times">www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.html</font></a><font color="black" face="Times New Roman,Georgia,Times">.</font><font color="black" face="Verdana,Arial,Helvetica,Geneva,Chicago" size="2">—</font><font size="2" color="black" face="Arial,Helvetica,Geneva,Swiss,SunSans-Regular">DW</font><font color="black" face="Verdana,Arial,Helvetica,Geneva,Chicago" size="2"><br>
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</font></p>
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</div>
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<p><font size="2" color="#0033cc" face="Verdana,Arial,Helvetica,Geneva,Chicago"><b><em><br>
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</em></b></font><br>
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</p>
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<div align="right">
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<p><a href="blast.html"><img height="27" width="69" src="images/continue.gif" border="0" alt="Continue"></a><br>
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