On 13:24 Sat 07 Feb , Paul Emsley wrote: > hari jayaram wrote: > Are the residues in helical secondary structure? (the DSSP algorithm is > built in to Coot - perhaps Pymol uses something else to define ss?)
PyMol indeed has its own algorithm. Here is a brief paste from it:
./layer3/Selector.c:
int SelectorAssignSS(PyMOLGlobals *G,int target,int present,int state_value,int
preserve,int quiet)
{
/* PyMOL's secondary structure assignment algorithm:
General principal -- if it looks like a duck, then it's a duck:
I. Helices
- must have reasonably helical geometry within the helical span
- near-ideal geometry guarantees helix assignment
- a continuous ladder stre i+3, i+4, or i+5 hydrogen bonding
with permissible geometry can reinforce marginal cases
- a minimum helix is three residues with i+3 H-bond
II. Sheets
- Hydrogen bonding ladders are the primary guide
- Out-of-the envelope
- 1-residue gaps in sheets are filled unless there
is a turn.
*/
--
Thanks,
Donnie
Donnie Berkholz
Developer, Gentoo Linux
Blog: http://dberkholz.wordpress.com
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