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So yes, we are willing to incorporate a strut algorithm into UCSF
Chimera, but right now, that code would need to be written by
someone else. I suspect that George Phillip's original Python code
would be a better starting point than the Jmol Java code. Another
good starting point would be the pioneering work done by MSOE that
is given in their RasMol Training Guide, Section III, "Designing a
Model to be Built on the Rapid Prototyping Machines", <a
href="http://www.rpc.msoe.edu/cbm/resources/rasmol.php">http://www.rpc.msoe.edu/cbm/resources/rasmol.php</a>.<br>
<br>
-- Greg<br>
<br>
On 04/17/2011 01:18 PM, <a class="moz-txt-link-abbreviated" href="mailto:moneal@notes.cc.sunysb.edu">moneal@notes.cc.sunysb.edu</a> wrote:
<blockquote
cite="mid:OFE29E2FA7.DBB108B6-ON852577D7.00772261-85257875.006F91C4@notes.cc.sunysb.edu"
type="cite"><font size="2" face="sans-serif">Hello,</font>
<br>
<br>
<font size="2" face="sans-serif">We just purchased a Zcorp 650, </font><a
moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true" 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
moz-do-not-send="true" 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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true" 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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true" name="12f548420460d22e_Bob_Hansen"></a><font
size="2" color="#004080" face="sans-serif">Hi,
Marvin!</font>
</p>
<p><font size="2" color="#004080" face="sans-serif"> </font>
</p>
<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>
<p><font size="2" color="#004080" face="sans-serif"> </font>
</p>
<p><img src="cid:part1.02020701.00040204@cgl.ucsf.edu"
height="150" width="250">
</p>
<p><font size="2" color="#004080" face="sans-serif"> </font>
</p>
<p><font size="2" color="#004080" face="sans-serif">Margaret</font>
</p>
<p><font size="2" color="#004080" face="sans-serif"> </font>
</p>
<p><font size="2" face="sans-serif">From: </font><a
moz-do-not-send="true"
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 moz-do-not-send="true"
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>
<p><font size="2" face="sans-serif"> </font>
</p>
<p><font size="2" face="sans-serif">Hey Margaret,</font>
</p>
<p><font size="2" face="sans-serif"> </font>
</p>
<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>
<p><font size="2" face="sans-serif"> </font>
</p>
<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>
<p><font size="2" face="sans-serif"> </font>
</p>
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="tel:%28631%29%20632-1680" target="_blank"><font size="2"
color="blue" face="sans-serif">(631)
632-1680</font></a>
</p>
<p>
</p>
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