<font size=2 face="sans-serif">Hello,</font>
<br>
<br><font size=2 face="sans-serif">We just purchased a Zcorp 650, </font><a href="http://www.zcorp.com/en/Products/3D-Printers/ZPrinter-650/spage.aspx"><font size=2 face="sans-serif">http://www.zcorp.com/en/Products/3D-Printers/ZPrinter-650/spage.aspx</font></a><font size=2 face="sans-serif">
and would like to begin building models of proteins. As you probably know,
when you print a physical model of a protein @ 100,000x scale on one of
these printers, it is very fragile. To help support the model, one must
place "Struts" in key locations. </font>
<br>
<br><font size=2 face="sans-serif">We currently use Jmol because it has
a strut algorithm built into the software. The algorithm is open source,
written originally by George Phillips and adapted by Bob Hanson (see email
below). But Stony Brook faculty are begging us to train our students on
Chimera and not JMol because (not surprisingly) most faculty at SBU use
Chimera and not JMol.</font>
<br>
<br><font size=2 face="sans-serif">My question: would you be willing to
incorporate this algorithm into Chimera (or does it already exist)? This
would allow Chimera to output pdb files that are ready for rapid prototyping,
a blossoming field: </font><a href="http://www.economist.com/node/18114327?story_id=18114327&CFID=162504503&CFTOKEN=65134946"><font size=2 face="sans-serif">http://www.economist.com/node/18114327?story_id=18114327&CFID=162504503&CFTOKEN=65134946</font></a>
<br>
<br><font size=2 face="sans-serif">I look forward to your response,</font>
<br><font size=2 face="sans-serif">Marvin</font>
<br>
<br>
<br><font size=2 face="sans-serif">Marvin H. O'Neal III, Ph.D.<br>
Undergraduate Biology<br>
108 CMM/BLL<br>
Stony Brook University<br>
Stony Brook, NY 11794-5110<br>
Phone: (631) 632-1326<br>
Fax: (631) 632-1680</font>
<br>
<br>
<br><font size=3>Sure, why not! It's not my algorithm, though. See </font><a href=http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java><font size=3 color=blue>http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java</font></a><font size=3><br>
<br>
125 //<br>
126 // Struts calculation (for rapid prototyping)<br>
127 //<br>
128 ///////////////////////////////////////////////////////////<br>
129 /**<br>
130 *<br>
131 * Algorithm of George Phillips </font><a href=mailto:phillips@biochem.wisc.edu><font size=3 color=blue>phillips@biochem.wisc.edu</font></a><font size=3><br>
132 *<br>
133 * originally a contribution to pyMol as struts.py;<br>
134 * adapted here by Bob Hanson for Jmol 1/2010<br>
135 *<br>
136 * Return a vector of support posts for rapid prototyping
models<br>
137 * along the lines of George Phillips for Pymol except
on actual molecular<br>
138 * segments (biopolymers), not PDB chains (which
may or may not be<br>
139 * continuous).<br>
<br>
<br>
Bob<br>
</font>
<br><font size=3>On Thu, Apr 14, 2011 at 9:57 AM, <</font><a href=mailto:moneal@notes.cc.sunysb.edu><font size=3 color=blue>moneal@notes.cc.sunysb.edu</font></a><font size=3>>
wrote:</font>
<br><font size=2 face="sans-serif">Bob,<br>
<br>
I teach introductory biology labs at Stony Brook and use physical models
to introduce students to research. I have used Ras-Mol but recently switched
to Chimera. I would like to share your strut algorithm with the Chimera
group in hopes that they will incorporate it into the software.<br>
<br>
Would you be willing to work with me on this?<br>
<br>
Marvin<br>
<br>
Marvin H. O'Neal III, Ph.D.<br>
Undergraduate Biology<br>
G-05 CMM/BLL<br>
Stony Brook University<br>
Stony Brook, NY 11794-5110<br>
Phone: </font><a href="tel:%28631%29%20632-1326" target=_blank><font size=2 color=blue face="sans-serif">(631)
632-1326</font></a><font size=2 face="sans-serif"><br>
Fax: </font><a href="tel:%28631%29%20632-1680" target=_blank><font size=2 color=blue face="sans-serif">(631)
632-1680</font></a><font size=2 face="sans-serif"><br>
</font><font size=2 color=#a1009f face="sans-serif"><br>
-----Forwarded by Marvin O'Neal/CAS on 04/14/2011 10:45AM -----</font>
<br><font size=2 face="sans-serif">To: </font><a href=mailto:moneal@notes.cc.sunysb.edu target=_blank><font size=2 color=blue face="sans-serif">"moneal@notes.cc.sunysb.edu"</font></a><font size=2 face="sans-serif">
</font><a href=mailto:moneal@notes.cc.sunysb.edu target=_blank><font size=2 color=blue face="sans-serif"><moneal@notes.cc.sunysb.edu></font></a><font size=2 face="sans-serif"><br>
From: "Franzen, Margaret" </font><a href=mailto:franzen@msoe.edu target=_blank><font size=2 color=blue face="sans-serif"><franzen@msoe.edu></font></a><font size=2 face="sans-serif"><br>
Date: 04/13/2011 01:56PM<br>
Subject: RE: strut algorithm<br>
(See attached file: Bob Hansen.vcf)<br>
<br>
</font>
<p><a name=12f548420460d22e_Bob_Hansen></a><font size=2 color=#004080 face="sans-serif">Hi,
Marvin!</font>
<p><font size=2 color=#004080 face="sans-serif"> </font>
<p><font size=2 color=#004080 face="sans-serif">Your earlier question now
makes sense! Bob Hansen is the Jmol guru who teaches Chemistry at St. Olaf
– and breathes life into all things Jmol. His contact is below:</font>
<p><font size=2 color=#004080 face="sans-serif"> </font>
<p><img src=cid:_2_0AB42BA00AB42894006F91BF85257875 width=250 height=150>
<p><font size=2 color=#004080 face="sans-serif"> </font>
<p><font size=2 color=#004080 face="sans-serif">Margaret</font>
<p><font size=2 color=#004080 face="sans-serif"> </font>
<p><font size=2 face="sans-serif">From: </font><a href=mailto:moneal@notes.cc.sunysb.edu target=_blank><font size=2 color=blue face="sans-serif">moneal@notes.cc.sunysb.edu</font></a><font size=2 face="sans-serif">
[</font><a href=mailto:moneal@notes.cc.sunysb.edu target=_blank><font size=2 color=blue face="sans-serif">mailto:moneal@notes.cc.sunysb.edu</font></a><font size=2 face="sans-serif">]
<br>
Sent: Wednesday, April 13, 2011 12:51 PM<br>
To: Franzen, Margaret<br>
Subject: RE: strut algorithm</font>
<p><font size=2 face="sans-serif"> </font>
<p><font size=2 face="sans-serif">Hey Margaret,</font>
<p><font size=2 face="sans-serif"> </font>
<p><font size=2 face="sans-serif">My question about the Strut command in
Jmol was specific to the math of the algorithm. I was looking for
the equation that runs in the background when a student types this command.
I couldn't find it in the documentation guide.</font>
<p><font size=2 face="sans-serif"> </font>
<p><font size=2 face="sans-serif">Do you have Bob's email? There seem to
be several Bob Hanson's on the internet.</font>
<p><font size=2 face="sans-serif"> </font>
<p><font size=2 face="sans-serif">Marvin<br>
<br>
Marvin H. O'Neal III, Ph.D.<br>
Undergraduate Biology<br>
G-05 CMM/BLL<br>
Stony Brook University<br>
Stony Brook, NY 11794-5110<br>
Phone: </font><a href="tel:%28631%29%20632-1326" target=_blank><font size=2 color=blue face="sans-serif">(631)
632-1326</font></a><font size=2 face="sans-serif"><br>
Fax: </font><a href="tel:%28631%29%20632-1680" target=_blank><font size=2 color=blue face="sans-serif">(631)
632-1680</font></a>
<p>