We just purchased a Zcorp 650, http://www.zcorp.com/en/Products/3D-Printers/ZPrinter-650/spage.aspx 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.
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.
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: http://www.economist.com/node/18114327?story_id=18114327&CFID=162504503&CFTOKEN=65134946
I look forward to your response,
Marvin
Marvin H. O'Neal III, Ph.D.
Undergraduate Biology
108 CMM/BLL
Stony Brook University
Stony Brook, NY 11794-5110
Phone: (631) 632-1326
Fax: (631) 632-1680
Sure, why not! It's not my algorithm, though. See http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java
125 //
126 // Struts calculation (for rapid prototyping)
127 //
128 ///////////////////////////////////////////////////////////
129 /**
130 *
131 * Algorithm of George Phillips phillips@biochem.wisc.edu
132 *
133 * originally a contribution to pyMol as struts.py;
134 * adapted here by Bob Hanson for Jmol 1/2010
135 *
136 * Return a vector of support posts for rapid prototyping models
137 * along the lines of George Phillips for Pymol except on actual molecular
138 * segments (biopolymers), not PDB chains (which may or may not be
139 * continuous).
Bob
On Thu, Apr 14, 2011 at 9:57 AM, <moneal@notes.cc.sunysb.edu> wrote:
Bob,
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.
Would you be willing to work with me on this?
Marvin
Marvin H. O'Neal III, Ph.D.
Undergraduate Biology
G-05 CMM/BLL
Stony Brook University
Stony Brook, NY 11794-5110
Phone: (631) 632-1326
Fax: (631) 632-1680
-----Forwarded by Marvin O'Neal/CAS on 04/14/2011 10:45AM -----
To: "moneal@notes.cc.sunysb.edu" <moneal@notes.cc.sunysb.edu>
From: "Franzen, Margaret" <franzen@msoe.edu>
Date: 04/13/2011 01:56PM
Subject: RE: strut algorithm
(See attached file: Bob Hansen.vcf)
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:
Margaret
From: moneal@notes.cc.sunysb.edu
[mailto:moneal@notes.cc.sunysb.edu]
Sent: Wednesday, April 13, 2011 12:51 PM
To: Franzen, Margaret
Subject: RE: strut algorithm
Hey Margaret,
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.
Do you have Bob's email? There seem to be several Bob Hanson's on the internet.
Marvin
Marvin H. O'Neal III, Ph.D.
Undergraduate Biology
G-05 CMM/BLL
Stony Brook University
Stony Brook, NY 11794-5110
Phone: (631)
632-1326
Fax: (631)
632-1680
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