<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">"Yang, Zheng (YZ)" <<a href="mailto:yz@cgl.ucsf.edu">yz@cgl.ucsf.edu</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">May 10, 2010 12:55:03 AM PDT<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Daniel Gurnon <<a href="mailto:danielgurnon@depauw.edu">danielgurnon@depauw.edu</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: [Chimera-users] presets, python and printing</b><br></span></div><br><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Dan,<div><br></div><div>I am using Chimera output STL files, then print out with a uPrintPlus 3D printer. It's pretty handy using the "Export Scene" function to convert models into STL files. Although each single part cannot have mixed color, the printer is capable of printing 8 color APS by changing the cartridge. I have tried various protein representations: surface, ribbons showing the secondary structures, etc. All of them work prefect. </div><div><br></div><div>By going over the Getting Started tutorial (<a href="http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html">http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html</a>), users can easily get familiar with Chimera. Your students can use either GUI or command line mode. Alternatively, you can prepare them a Chimera commands file (plain text scripts file), containing your preset, bond thickness. (<a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/indexcommand.html#cmdfile">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/indexcommand.html#cmdfile</a>) They just need to open and load it. </div><div><br></div><div>Chimera has the Undo Move function, allowing backtracking through the most recent model positions. (<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/undomove/undomove.html">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/undomove/undomove.html</a>) Section saving may solve part of the "Undo" problem. </div><div><br></div><div>Looking forward to collaborating with you on the 3D model printing. </div><div><br></div><div>Best,</div><div>YZ</div><div><br></div><div><br></div><div><br></div><div><br></div><div><br></div><div> </div><div><br><div><div>On May 9, 2010, at 7:51 AM, Daniel Gurnon wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hello everyone,<br>My colleague and I are planning to incorporate 3D physical models into the introductory biochemistry course at our university, and I want students to use Chimera in the design of models. I've seen the technotes on 3D models made by the uPrint printer (<a href="http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html">http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html</a>). We'll hopefully be collaborating with the folks at MSOE on this, using their Z-corporation printer. They use RasMol to design models, but the file read by the printer is in .stl format.<br>
<br>Here are my questions:<br>1) Has anyone used Chimera to create models to be printed on a Z-corp printer? (if yes, I'll have many more questions for you...)<br><br>2) Is it possible to define a user preset in Chimera with Python? I know this isn't currently possible with chimera commands, and I am *just* getting into Python now. Because students have difficulty jumping in to a project like this if they first have to learn to enter commands at a prompt, I want to make some presets that apply settings compatible with a 3D model; bond thickness, colors, etc.<br>
<br>3)If one knew Python, would it be possible to design a simplified user interface for Chimera? Even as simple as a pop-up window that contained the key features I want students to have access to right away?<br><br>4) Probably the biggest drawback to using Chimera with undergrads is the lack of an "Undo" button. I'm guessing this is extremely difficult to implement because of all 3rd party extensions incorporated into Chimera? What about an option to autosave every five or ten minutes?<br>
<br>Thanks<br>Dan<br clear="all"><br>-- <br>____________________________<br><br>Daniel Gurnon, Ph. D.<br>Assistant Professor of Chemistry<br>DePauw University<br>Greencastle, IN 46135<br><br>p: 765-658-6279<br>e: <a href="mailto:danielgurnon@depauw.edu">danielgurnon@depauw.edu</a><br>
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