[chimera-dev] Monitor lines

Tue Apr 19 17:27:01 PDT 2011

Just to add a little more information, the main steps would be:

(A) identify atom pairs to connect, automatically with an algorithm or interactively
(B) create pseudobonds connecting the pairs
(C) draw the pseudobonds as sticks and possibly make them fatter

I'm not a programmer, so here's an example in Chimera commands... but all of these things can also be done in Python code, as Eric described for (B).  Say the protein is shown as a ribbon and you have identified residue pairs to be connected. You could use the alpha-carbons as connection points. Chimera commands could be something like:

# connect residues 14 and 27 in chain A with distance pseudobond
dist :14.a at ca :27.a at ca

# connect residue 40 in chain A and residue 258 in chain B
dist :40.a at ca :258.b at ca

# hide distance labels, draw as sticks, make sticks fatter
setattr p label " "
setattr p drawMode 1
setattr p radius .4

Chimera commands can be typed into the Command Line, or a series of them placed (with or without the comment lines that start with #) into a plain text file named something.com, which when opened in Chimera executes the commands.
Elaine

On Apr 19, 2011, at 4:25 PM, Eric Pettersen wrote:

> 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
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Chimera-dev mailing list
>>> 
>>> Chimera-dev at cgl.ucsf.edu
>>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>> 
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