This is going to be an interesting challenge, and I will need the help
of some biomolecular scientist types.
Someone explain to me how psi and phi are related to helix structure.
The problem is, I think, that Jmol is two-fold:
1) Jmol is using a very simplistic idea of what a helix is
2) Jmol does not recognize that although there is a broad range of
possibilities for phi and psi, a given helix should only have a certain
subset of that range.
3) Once a residue is assigned "helix" it doesn't matter what subtype it is.
Bob
[EMAIL PROTECTED] wrote:
>Quoting Bob Hanson <[EMAIL PROTECTED]>:
>
>
>
>>Herráez Sánchez Angel wrote:
>>
>>
>>
>>>I found a funny behaviour of "rockets" on 2hhd.pdb, chain C
>>>
>>>
>
>
>
>>I'm not seeing what you want me to see.
>>
>>load 2hhd.pdb;display *:C;center visible;
>>restrict none;select hetero and not solvent;wireframe on
>>select protein;cartoons on;rockets on
>>select 74;color yellow
>>moveto 1.0 { 494 537 684 93.7} 200.0 {-0.3075999 23.937828 48.634956} 52.4;
>>
>>This looks perfectly fine to me. The turn at 74 is there.
>>
>>I got my 2hhd.pdb file from the AJAX connection at
>>
>>http:www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm
>>
>>Do we have the same files?
>>
>>
>>
>
>If I use the PDB format file provided by the RCSB FTP server for the
>asymmetric unit I observe the same as Angel. If I use the PDB format
>file of the biological unit the helix is split up into 3 helices.
>
>Comparison of the files shows that the asymmetric unit file doesn't
>contain any secondary structure records but the biological unit file
>does.
>
>Regards,
>Rolf
>
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