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).New versions of Jmol use DSSP calculation.Old versions of Jmol used Ramachandran-angle based calculation.If the pdb or mmcif file des not contain HELIX/SHEET/TURN information:.In new Jmol versions, pdb and mmcif readers also read helix types alpha, pi, and 3 10, and color them slightly differently (see colors below). If the pdb or mmcif file contains HELIX/SHEET/TURN information: that information is respected in all Jmol versions.15: 7841-7864 doi:10.3390/ijms15057841 Implemented at To use DSSP 1.0 instead, you may use calculate structure DSSP 1.0, show DSSP 1.0, load. Rob van der Kant, Gert Vriend (2014) Int. This change only affects helices that have bulges, indicating them more appropriately as pi helices rather than alpha helices. Starting with Jmol 14.6 the new DSSP 2.0 algorithm is used. This is accompanied by some changes in the defaults and some new commands. Starting with versions 12.0.18 and 12.1.15, Jmol implements the DSSP algorithm for determination of secondary structure in proteins. See Quality and speed Molecular surfacesĭocumentation and testing page Secondary structure Responsiveness to user interaction and quality of the rendering may be adjusted using several options or parameters in JmolScript. 3.2.3 Customization of the Secondary Structure for Regions.
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