[chimera-dev] Monitor lines

[moneal at notes.cc.sunysb.edu]

Hello,

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 at 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 at 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 at notes.cc.sunysb.edu" <moneal at notes.cc.sunysb.edu>
From: "Franzen, Margaret" <franzen at msoe.edu>
Date: 04/13/2011 01:56PM
Subject: RE: strut algorithm
(See attached file: Bob Hansen.vcf)


Hi, Marvin!
 
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 at notes.cc.sunysb.edu [mailto:moneal at 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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