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° | ShowRota<Res|Mol|Obj|All> | - |
Show side-chain rotamers |
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| | | Command | | Argument |
| Datatype | | Default | | Min | | Max | |
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| Format: | | ShowRota<Res|Mol|Obj|All> | Selection | | SELECTION | | - |
| - | | - | | |
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| Python: | | resultlist = ShowRota<Res|Mol|Obj|All>(selection1) | | ||||||||||
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| Menu: | | Analyze > Rotamers of | | ||||||||||
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| Related: | | Check | | ||||||||||
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| Required: | |  | |
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This command maps to WHAT IF's DGROTA option. WHAT IF takes the fragment of five residues with the selected residue in the middle and searches the database for equally long fragments with a highly similar backbone conformation. Highly similar typically means that the RMSD on Calpha atoms is lower than
0.7 A.
Then a new object is created, which contains all the possible side-chain conformations of the selected residue,
colored from blue (best backbone fit) to yellow (worst backbone fit).
This command ignores the environment, e.g. possible bumps, as well as the two N- and C-terminal residues.
The created objects consist of points and lines that can be styled with the
PointPar command. They are not linked to the atoms they originated from,
and are thus not clickable. If you want to obtain real rotamers that are part of the soup,
then use the SampleDih command.
For each rotamer, a new object is created. As YASARA's limit is
250 objects, that is also the maximum number of residues whose rotamers can be shown at the same time.
Example 1:
ShowRotaRes Tyr 106
Show the backbone-dependent rotamer distribution for residue Tyr
106.
Example 2:
ShowRotaObj 1crn
Show the rotamer distributions for all residues in object
1crn.
Example 3:
rotlist() = ShowRotaMol A
Show the rotamer distributions for all residues in molecule A and assign the numbers of the created objects to the list
'rotlist'.
Example macro:
# EXAMPLE ShowRota # Requires the Twinset Clear # Style 1crn LoadPDB 1crn Style Trace ColorBonds grey # Show all side-chain rotamers ShowRota # Style the side-chain rotamers PointPar Radius=5,plastic=Yes # Orient the object Pos Y=-1,Z=24 Ori 214,29,10
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| Figure: Result of the example macro above. |