This subcommunity is for Jmol users that use Jmol for display and analysis of protein structures. Please add on this page your favorite scripts etc. for displaying proteins in Jmol.
- Angel Herraez page
- Eric Martz: FirstGlance in Jmol is a simple tool for exploring the structure of any on-line macromolecular model. Protein Explorer exports molecular views into Jmol, see MolSlides.Org
Starting with versions 12.0.18 and 12.1.15, Jmol implements the DSSP algorithm for determination of secondary structure in proteins. This is accompanied by some changes in the defaults and some new commands.
When reading files
- If the PDB or mmCIF file contains HELIX/SHEET/TURN information: that information is respected in all Jmol versions. In new Jmol versions, PDB and CIF readers also read helix types 1 (alpha), 3 (pi), and 5 (3_10), and color them slightly differently.
- If the PDB or mmCIF file des not contain HELIX/SHEET/TURN information:
- Old versions of Jmol used Ramachandran-angle based calculation.
- New versions of Jmol use DSSP calculation.
- In the case of alpha-carbon-only chains, all versions of Jmol use the method of Levitt and Greer. doi
- In new versions of Jmol the Ramachandran-angle-based calculation is still available (see below).
Forced recalculation of structure
This command overwrites any secondary structure assignment with a new one:
- In old Jmol versions, calculated using the Ramachandran method.
- In new Jmol versions, calculated using the DSSP method.
calculate structure ramachandranis available for forcing the old method of calculation (it may have some advantages in certain contexts). It can be shortened to
calculate structure rama.
calculate hBonds structuredoes DSSP determining hydrogen bonds only.
set defaultStructureDSSP falsewill change the defaults of file load and
calculate structureto use the Ramachandran method; by default, it is true and uses the DSSP method.
set dsspCalculateHydrogenAlways falsedoes 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.
show dsspdisplays a report of the DSSP calculation.
set debugdisplays a verbose DSSP calculation.
save structure s1(for example) saves in memory the current structure assignment with the internal ID 's1' for later restoring.
restore structure s1restores the previously saved assignment.
Selection and coloring
color structurenow applies different shades of color to alpha, 3_10 and pi helices.
select helixincludes all 3 types of helices.
select helix310(example: 2JC9.pdb)
select helixPi(example: 2JC9.pdb)
select substructure=7matches DSSP "G", i.e. 3_10 helices, same as
select substructure=8matches DSSP "H", i.e. alpha helices, same as
select substructure=9matches DSSP "I", i.e. pi helices, same as
label %[substructure]labels with the texts: helixalpha, helix310, helixpi, sheet, turn, none
- M. Levitt and J. Greer (1977) Automatic identification of secondary structure in globular proteins. J. Mol. Biol. 114: 181-239. doi:10.1016/0022-2836(77)90207-8
- Helix types in PDB format: columns 39-40, right-justified.
substructure and name
|right-handed alpha, 412 (default)||1||H||8 helixAlpha|
|right-handed pi||3||G||7 helixPi|
|right-handed 310||5||I||9 helix310|
|(beta) strand||E||2 sheet|
|isolated beta-bridge residue||B|