[chimera-dev] Monitor lines

Tue Apr 19 16:25:56 PDT 2011

If you do decide to try to implement it yourself, you could write it  
as a Chimera Python script that creates "pseudobonds" for the struts  
you need.  You would get a pseudobond group for the struts with this  
call:

	from chimera.misc import getPseudoBondGroup
	pbg = getPseudoBondGroup("struts")

You would then add a pseudobond between atoms a1 and a2 with:

	pbg.newPseudoBond(a1, a2)

The pseudobonds would be treated the same as all other pseudobonds  
(e.g. hydrogen bonds, distance monitors) and would appear in Chimera's  
X3D/STL/VRML output.

You could ask further scripting questions on this list.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Apr 19, 2011, at 2:53 PM, Greg Couch wrote:

> 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.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:
>>
>>
>> <mime-attachment.jpeg>
>>
>>
>> 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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