label % labels with the texts: helixalpha, helix310, helixpi, sheet, turn, none.color structure now applies different shades of color to alpha, 3 10 and pi helices, in addition to the classic coloring of helices, beta strands, turns and unstructured portions (see colors below).For ex., select substructure=2 selects beta strands, but select structure=8 selects nothing. Note: it is safe to use substructure for all selection commands. Example: 2JC9.pdbĮxample: 2JC9.pdb after calculate structure Matches unstructured protein (random coil) structure helix310 That does not perfectly match that defined in the published crystal or NMR structure. Often such adjustments may be useful when the structure assignment informationįormerly in the file has been removed as result of some processing of the PDB file and the default structure detection results in a secondary structure Obviously these adjustments are to be used sparingly as there is often a reason the secondary structure detection methods within Jmolįail to identify the structure and you don't want to make erroneous assignments. select 16-31:A structure HELIX cartoon on to define residues 16-31 of chain A as an alpha helix for cartoon style display.Select the portion you want to change first. restore structure s1 restores the previously saved assignment.Ĭustomization of the Secondary Structure for RegionsĪs described here, you can can define individual secondary structure elements as well.save structure s1 (for example) saves in memory the current structure assignment with the internal ID 's1' for later restoring.set debug displays a verbose DSSP calculation.show dssp displays a report of the DSSP calculation.set dsspCalculateHydrogenAlways false does DSSP enforcing the use of backbone amide H atoms present in the file by default, it is true and does standard DSSP, ignoring all backbone amide H atoms present in the file and using rough approximations instead.set defaultStructureDSSP false will change the defaults of file load and calculate structure to use the Ramachandran method by default, it is true and uses the DSSP method.calculate hBonds structure does DSSP determining hydrogen bonds only.It can be shortened to calculate structure rama. calculate structure ramachandran is available for forcing the old method of calculation (it may have some advantages in certain contexts).Using the command set structure described here you can define the minimum and maximum psi values that would be valid for each structure type. So, you will usually want to follow it with cartoons on or something of the sort. Note that, intentionally, Jmol turns off all bioshapes when the calculate structure command is given. In new Jmol versions, calculated using the DSSP method.In old Jmol versions, calculated using the Ramachandran method.
This command overwrites any secondary structure assignment with a new one: In new versions of Jmol the calculation based on Ramachandran angles is still available (see below).įorced recalculation of structure calculate structure.In the case of alpha-carbon-only chains, all versions of Jmol use the method of Levitt and Greer ( doi).
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