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@ca :27.a@ca

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

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/modelset...

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)

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@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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It's a web site: www.something.com. Mail is just trying to be helpful to you. You and I are old enough to know that command files had the .com suffix long before the world wide web existed, but I guess the mail app isn't as old. :-)

--tom

On 4/19/11 5:31 PM, Elaine Meng wrote:

Interesting, something [dot] com appeared as a link in my incoming mail -- I didn't make that URL or a file, so no need to click on it! Annoying! Elaine

On Apr 19, 2011, at 5:27 PM, Elaine Meng wrote:

...

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.

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