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===DESCRIPTION===
 
===DESCRIPTION===
 +
'''dss''' ''d''efines ''s''econdary ''s''tructure based on backbone geometry and hydrogen bonding patterns. 
 
   
 
   
  "dss" defines secondary structure based on backbone geometry
+
With PyMOL, heavy emphasis is placed on cartoon aesthetics, and so both hydrogen bonding patterns and backbone geometry are used in the assignment process.  Depending upon the local context, helix and strand assignments are made based on geometry, hydrogen bonding, or both.
  and hydrogen bonding patterns.
 
 
   
 
   
  With PyMOL, heavy emphasis is placed on cartoon aesthetics, and so
+
This command will generate results which differ slightly from DSSP and other programs.  Most deviations occur in borderline or transition regions.  Generally speaking, PyMOL is more strict, thus assigning fewer helix/sheet residues, except for partially distorted helices, which PyMOL tends to tolerate.
  both hydrogen bonding patterns and backbone geometry are used in
 
  the assignment process.  Depending upon the local context, helix
 
  and strand assignments are made based on geometry, hydrogen
 
  bonding, or both.
 
 
  This command will generate results which differ slightly from DSSP
 
  and other programs.  Most deviations occur in borderline or
 
  transition regions.  Generally speaking, PyMOL is more strict, thus
 
  assigning fewer helix/sheet residues, except for partially
 
  distorted helices, which PyMOL tends to tolerate.
 
 
 
  WARNING: This algorithm has not yet been rigorously validated.
 
 
    
 
    
 +
WARNING: This algorithm has not yet been rigorously validated.
 +
 
===USAGE===
 
===USAGE===
 
+
dss selection, state
  dss selection, state
+
 
+
state = state-index or 0 for all states
  state = state-index or 0 for all states
+
 
 
 
 
===EXAMPLES===
 
===EXAMPLES===
  dss
+
<source lang="python">
+
# determine secondary structures in
 +
# all loaded objects in PyMOL
 +
dss
 +
</source>
 +
 
 
===NOTES===
 
===NOTES===
If you dislike one or more of the assignments made by dss, you can
+
If you dislike one or more of the assignments made by dss, you can use the alter command to make changes (followed by "rebuild").
use the alter command to make changes (followed by "rebuild").
 
 
For example:
 
For example:
      alter 123-125/, ss='L'
+
<source lang="python">
      alter pk1, ss='S'
+
# set residues 123-125 as being loops
      alter 90/, ss='H'
+
alter 123-125/, ss='L'
      rebuild  
+
 
 +
# set the secondary structure of selection (pk1) to beta sheet
 +
alter pk1, ss='S'
 +
 
 +
# set residue 90 to be alpha-helical
 +
alter 90/, ss='H'
 +
 
 +
# update the scene in PyMOL to reflect the changes.
 +
rebuild  
 +
</source>
 +
 
 +
====Secondary Structure Determination====
 +
As is typical with PyMOL, the secondary structure assignment engine is ad hoc and empirically tuned to produce desirable aesthetics.  Though there are some phi/psi's that are clearly helix/sheet and others that are clearly not, there are certain regions of phi/psi space were the assignment is subjective or arbitrary.  In my experience, algorithms based on strict definitions tend to operate poorly in such regions, and so PyMOL's algorithm is "fuzzy" in that there is a grey area where residues may be accepted or rejected as helix/sheet depending upon the surrounding context. 
 +
 
 +
There aren't any hard & fast definitions.  But you are welcome to check out the collection of settings beginning with "ss_helix" and "ss_strand", noting that the include and exclude settings are deviations around the target in degrees.  If you think PyMOL is incorrectly assigning secondary structure, then you might try varying these.
 +
 
 
   
 
   
[[Category:Commands|dss]]
+
[[Category:Commands|Dss]]
 +
[[Category:Biochemical_Properties|Dss]]
 +
[[Category:States|Dss]]

Revision as of 13:47, 20 June 2009

DESCRIPTION

dss defines secondary structure based on backbone geometry and hydrogen bonding patterns.

With PyMOL, heavy emphasis is placed on cartoon aesthetics, and so both hydrogen bonding patterns and backbone geometry are used in the assignment process. Depending upon the local context, helix and strand assignments are made based on geometry, hydrogen bonding, or both.

This command will generate results which differ slightly from DSSP and other programs. Most deviations occur in borderline or transition regions. Generally speaking, PyMOL is more strict, thus assigning fewer helix/sheet residues, except for partially distorted helices, which PyMOL tends to tolerate.

WARNING: This algorithm has not yet been rigorously validated.

USAGE

dss selection, state

state = state-index or 0 for all states

EXAMPLES

# determine secondary structures in 
# all loaded objects in PyMOL
dss

NOTES

If you dislike one or more of the assignments made by dss, you can use the alter command to make changes (followed by "rebuild"). For example:

# set residues 123-125 as being loops
alter 123-125/, ss='L'

# set the secondary structure of selection (pk1) to beta sheet
alter pk1, ss='S'

# set residue 90 to be alpha-helical
alter 90/, ss='H'

# update the scene in PyMOL to reflect the changes.
rebuild

Secondary Structure Determination

As is typical with PyMOL, the secondary structure assignment engine is ad hoc and empirically tuned to produce desirable aesthetics. Though there are some phi/psi's that are clearly helix/sheet and others that are clearly not, there are certain regions of phi/psi space were the assignment is subjective or arbitrary. In my experience, algorithms based on strict definitions tend to operate poorly in such regions, and so PyMOL's algorithm is "fuzzy" in that there is a grey area where residues may be accepted or rejected as helix/sheet depending upon the surrounding context.

There aren't any hard & fast definitions. But you are welcome to check out the collection of settings beginning with "ss_helix" and "ss_strand", noting that the include and exclude settings are deviations around the target in degrees. If you think PyMOL is incorrectly assigning secondary structure, then you might try varying these.