It seems to me there will be a significant amount of minimization to be
done. That is beyond the scope of Jmol. Jmol can minimize small sections of
a model, but not a full protein.
On Wed, Apr 24, 2013 at 9:27 AM, Robert Hanson <[email protected]> wrote:
> 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 <[email protected]> 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
>
>
--
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
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