> >You can explain the algorithms to me and help test/debug the code.
> >
>
> o.k, I will be glad to help and test.
>
>
> there is already some helix assignment,
Yes, I did that ...
> if no secondary structure is
> in the PDB file, so it could be the basics already have been
> implemented,
I have tried several times :-)
> but let's start from the beginning:
>
> Secondary Structure is assigned usually by investigating the Hydrogen
Bond (H-Bonds) pattern and geometrical orientation of the backbone of a
protein.
Correct.
The hbonds that we are currently calculating are only those along the
backbone.
> To calculate an H-Bond one has to use the C,O atoms of one amino acid
and the N,H atoms of a second one. Since most protein structures are
determinde with H-atoms, the first step of an algorithm would be to
create "virtual" H-atoms.
This part is done.
You can load up a .pdb or .mmcif file and say:
hbonds on; color hbonds yellow
in order to see how the hbonds are being assigned.
It only works for the amino backbone, but I think that it is basically
correct.
> After the H-Bonds have been calculated the algorithm would look for
patterns of H-Bonds, that are typical for Secondary structure
> elements. E.g H-Bonds from amino acid i to amino acid i+4 are typical
for alpha helices.
>
> * Do you already calculate H-atoms and H-Bonds in Jmol?
Yes
I think that the helices use i + 4, i + 3, and i + 5
> >You don't need to do the actual coding ... unless you want to.
>
> I can imagine to contribute some parts, but everything is too much. I am
not familiar with the details of Jmol. The actual rules for
> assignment in general are not too difficult, but a lot of exception
handling is required since PDB files are very inconsistent. E.g. One
always
> has to check that amino acids contain all required atoms, are
> connected to each other, are not "proline", etc.
That testing is already taking place in Jmol and is quite robust.
> >One thing that I want to be very cautious about is
> licensing/intellectual
> >property rights. The Jmol code is very clean in this area.
> >However, code that you have developed would be very helpful.
>
> did some code based on the biojava protein structure code, but it is
still in very early stage.
>
> If I know better what is needed, I can contributes some parts.
If you could take a look at the hbonds that Jmol is calculating that would
be good.
Helixes are done ... I think.
I have had lots of problems with sheets.
Q: What are the patterns that I am looking for to identify sheets?
> e.g. howto calc H-atom using biojava:
>
[snip]
I will look at the code snippet that you sent.
> >
> >Q: Are you familiar with the RasMol/Chime/Jmol scripting language?
> >
>
> yes
>
> >
> >Q: What do you think about some commands like:
> > select {some stuff}; structure helix
> > select {some other stuff}; structure sheet
>
> looks very good to me.
good, then I will keep thinking about this.
Miguel
-----
Open Source Molecular Visualization
www.jmol.org
[EMAIL PROTECTED]
-----
-----
Open Source Molecular Visualization
www.jmol.org
[EMAIL PROTECTED]
-----
-------------------------------------------------------
This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
Use IT products in your business? Tell us what you think of them. Give us
Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more
http://productguide.itmanagersjournal.com/guidepromo.tmpl
_______________________________________________
Jmol-developers mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
