Editing Dss (section)

===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:
<source lang="python">
# 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 
</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:Biochemical_Properties|Dss]]
[[Category:States|Dss]]