<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span style="font-family: monospace; ">Hello everybody,</span><br style="font-family: monospace; "><span style="font-family: monospace; ">A new production release of UCSF Chimera (version 1.9) is available:</span><br style="font-family: monospace; "><a href="http://www.rbvi.ucsf.edu/chimera/download.html" style="font-family: monospace; ">http://www.rbvi.ucsf.edu/chimera/download.html</a><br style="font-family: monospace; "><br style="font-family: monospace; "><span style="font-family: monospace; ">Download is free for noncommercial use.</span><br style="font-family: monospace; "><span style="font-family: monospace; ">Platforms: Windows, Mac, Linux, including 64-bit versions (recommended</span><br style="font-family: monospace; "><span style="font-family: monospace; ">for working with large datasets on machines with at least 4GB memory).</span><br style="font-family: monospace; "><br style="font-family: monospace; "><span style="font-family: monospace; ">New features include multiple sequence alignment using Clustal Omega</span><br style="font-family: monospace; "><span style="font-family: monospace; ">or MUSCLE web services, building double-helical nucleic acids,</span><br style="font-family: monospace; "><span style="font-family: monospace; ">"colorkey" command, "struts" command to reinforce structures for</span><br style="font-family: monospace; "><span style="font-family: monospace; ">3D printing, "vseries" volume series playback and processing options,</span><br style="font-family: monospace; "><span style="font-family: monospace; ">more efficient save/restore of coordinates in sessions, Dynameomics </span><br style="font-family: monospace; "><span style="font-family: monospace; ">amino acid rotamer library, WMV2 movie output, COLLADA export.</span><br style="font-family: monospace; "><br style="font-family: monospace; "><span style="font-family: monospace; ">More details are given below; see release notes for the full list:</span><br style="font-family: monospace; "><a href="http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.9.html" style="font-family: monospace; ">http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.9.html</a><br style="font-family: monospace; "><br style="font-family: monospace; "><span style="font-family: monospace; ">Display, Interface:</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* icon for menu selection mode: Append, Intersect, Replace, Subtract</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* distance monitor line style and color can be saved as preferences</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* silhouette outlines can be controlled per-model </span><br style="font-family: monospace; "><span style="font-family: monospace; ">* Axes/Planes/Centroids objects can be recolored with Actions menu</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* "colorkey" command implementation of Color Key tool</span><br style="font-family: monospace; "><br style="font-family: monospace; "><span style="font-family: monospace; ">Structure Analysis and Modeling:</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* new Align Chain Sequences tool for multiple sequence alignment of</span><br style="font-family: monospace; "><span style="font-family: monospace; ">structure chains using a Clustal Omega or MUSCLE web service</span><br style="font-family: monospace; "><span style="font-family: monospace; ">(these can also be called to realign the sequences in an existing</span><br style="font-family: monospace; "><span style="font-family: monospace; ">Multalign Viewer window)</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* "mda" command to Blast-search and retrieve structures similar to</span><br style="font-family: monospace; "><span style="font-family: monospace; ">a query sequence, lay them out left->right by N->C along the query</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* APBS interface omits explicit solvent by default</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* "coulombic" command allows specifying atoms/charges to use for ESP</span><br style="font-family: monospace; "><span style="font-family: monospace; ">calculation independent of the surface to color</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* Build Structure tool allows generating nucleic acid double helices,</span><br style="font-family: monospace; "><span style="font-family: monospace; ">specifying phi angle when joining peptides</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* "adjust" command to change bond angle or length</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* MD Movie session support for partly loaded trajectories</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* Morph Conformations pairs chains by ID if the sets of IDs are same</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* "ramachandran" command can assign probabilities as attributes</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* Rotamers/swapaa include Dynameomics rotamer library (Daggett group)</span><br style="font-family: monospace; "><br style="font-family: monospace; "><span style="font-family: monospace; ">Volume Data (density maps, ESP maps):</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* "vop" volume operations to take pointwise maximum or multiply maps</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* "vseries" command options to open and close volume time series,</span><br style="font-family: monospace; "><span style="font-family: monospace; ">jump playback to a specific frame, perform various processing such</span><br style="font-family: monospace; "><span style="font-family: monospace; ">as alignment, normalization, cropping, compressing, save to file</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* new volume input format VTK structured points (ASCII)</span><br style="font-family: monospace; "><br style="font-family: monospace; "><span style="font-family: monospace; ">General, I/O:</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* some Preferences reorganization, new categories: Labels, Selection</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* more efficient save/restore of coordinates in sessions</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* new output movie format WMV2</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* new export formats COLLADA, VTK</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* "struts" command to add strengthening bonds for 3D printing</span><br style="font-family: monospace; "><span style="font-family: monospace; ">* "leap" command for using Chimera with a Leap Motion Controller</span><br style="font-family: monospace; "><br style="font-family: monospace; "><span style="font-family: monospace; ">Enjoy! On behalf of the Chimera team,</span><div><span style="font-family: monospace; "><br></span></div><div><span style="font-family: monospace; ">--Eric</span></div><br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span>
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