[chimera-dev] Monitor lines

Tue Apr 19 14:53:36 PDT 2011

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", 
http://www.rpc.msoe.edu/cbm/resources/rasmol.php.

     -- Greg

On 04/17/2011 01:18 PM, moneal at notes.cc.sunysb.edu wrote:
> Hello,
>
> We just purchased a Zcorp 650, 
> http://www.zcorp.com/en/Products/3D-Printers/ZPrinter-650/spage.aspxand 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 
> <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 
> <mailto: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 
> <mailto: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 <tel:%28631%29%20632-1326>
> Fax: (631) 632-1680 <tel:%28631%29%20632-1680>
>
> -----Forwarded by Marvin O'Neal/CAS on 04/14/2011 10:45AM -----
> To: "moneal at notes.cc.sunysb.edu" 
> <mailto:moneal at notes.cc.sunysb.edu><moneal at notes.cc.sunysb.edu> 
> <mailto:moneal at notes.cc.sunysb.edu>
> From: "Franzen, Margaret" <franzen at msoe.edu> <mailto: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>[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 <tel:%28631%29%20632-1326>
> Fax: (631) 632-1680 <tel:%28631%29%20632-1680>
>
>
> _______________________________________________
> Chimera-dev mailing list
> Chimera-dev at cgl.ucsf.edu
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-dev/attachments/20110419/f3f7083b/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 5406 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-dev/attachments/20110419/f3f7083b/attachment.jpe>