Re: [Jmol-users] Help with Project Direction

[Robert H. <ha...@st...>]

This sounds very interesting. When you do the folding, do you do it
strictly in terms of residue locations in space? That is, no real atoms? Or
is there at least a backbone to work with?


On Wed, Apr 24, 2013 at 1:54 AM, germoose <ge...@un...> wrote:

>
> Greetings,
>
> Previously I have created a program which takes a sequence of hydrophobic
> or
> hydrophilic amino acids and folds it based of the HP protein folding model.
> The folded coordinates are given and displayed in a x-y-z grid format (as
> in
> an amino acid can only be located on integer x, y, z coordinates; no
> decimals). A typical folded protein resembles this:
>
> http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
> http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
> http://ars.els-cdn.com/content/image/1-s2.0-S1476927108000327-gr2.jpg
>
> What I hoping to add is to use Jmol to display this protein. However,
> instead of simply a ball representing the amino acid, I would like to show
> each molecule of each amino acid.
>
> My current idea of how I would go about this is as such:
>
> - Read in a real protein sequence ( Lys - Asp - Arg - etc ), and turn this
> into a string of hydrophobic or hydrophilic amino acids for my program to
> fold.
> - Once folded, replace each amino acid with it's actual molecules in Jmol,
> to do this I might
>      - programmatically create a .pdb file for Jmol to read. To do this I
> would already have pdb files for all 20 amino acids stored, and displace
> their atoms to the grid coordinate given from the existing program.
> However,
> I would have to get the amino acids to be bonded together through peptide
> bonds, which seems tricky.
>
> Before I step into this large project, I would just like to ensure I'm on
> the right path and doing things the best/easiest way possible. I am quite
> new to Jmol and would very much appreciate any suggestions or things to
> look
> out for. If you have any questions, I am more than happy to answer them.
>
> Thank you for your time
> --
> View this message in context:
> http://old.nabble.com/Help-with-Project-Direction-tp35329120p35329120.html
> Sent from the jmol-users mailing list archive at Nabble.com.
>
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900