Protein Community

Jmol/JSmol Community

• Community & users
• Communities: Crystal · Protein · Quantum Chemistry · Solid State · Folding@home
• List of users & their pages

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. Proteopedia.Org is a Jmol-based wiki with easy Scene-Authoring Tools for creating and sharing customized molecular scenes without learning Jmol language.

Adjusting speed and quality

Responsiveness to user interaction and quality of the rendering may be adjusted using several options or parameters in JmolScript. See Quality and speed

Molecular surfaces

documentation and testing page

Secondary structure

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.

Starting with Jmol 14.6 the new DSSP 2.0 algorithm is used. This change only affects helices that have bulges, indicating them more appropriately as pi helices rather than alpha helices.

Rob van der Kant, Gert Vriend (2014) Int. J. Mol. Sci. 15: 7841-7864; doi:10.3390/ijms15057841

Implemented at http://www.cmbi.ru.nl/dssp.html

To use DSSP 1.0 instead, you may use calculate structure DSSP 1.0, show DSSP 1.0, load ... filter "DSSP1"

When reading files

1. 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 mmcif readers also read helix types alpha, pi, and 3₁₀, and color them slightly differently (see colors below).
2. 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.
3. In the case of alpha-carbon-only chains, all versions of Jmol use the method of Levitt and Greer (doi).
4. In new versions of Jmol the calculation based on Ramachandran angles is still available (see below).

Forced recalculation of structure

calculate 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.

Note that, intentionally, Jmol turns off all bioshapes when the calculate structure command is given. So, you will usually want to follow it with cartoons on or something of the sort.

Using the command set structure described here you can define the minimum and maximum psi values that would be valid for each structure type.

New commands

• calculate structure ramachandran is 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 structure does DSSP determining hydrogen bonds only.
• 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.
• 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.
• show dssp displays a report of the DSSP calculation.
• set debug displays 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 s1 restores the previously saved assignment.

Customization of the Secondary Structure for Regions

As described here, you can can define individual secondary structure elements as well. Select the portion you want to change first. For example,

• select 16-31:A; structure HELIX; cartoon on; to define residues 16-31 of chain A as an alpha helix for cartoon style display.

Obviously these adjustments are to be used sparingly as there is often a reason the secondary structure detection methods within Jmol fail to identify the structure and you don't want to make erroneous assignments. Often such adjustments may be useful when the structure assignment information formerly 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 that does not perfectly match that defined in the published crystal or NMR structure.

The commands:

• structure HELIX
• structure SHEET
• structure TURN
• structure helix310 <---NEED TO VERIFY WORKS.

Selection and coloring

Atom expressions related to secondary structure:

by name		by index
		select structure=-1	matches non-protein parts (ligands,...)
		select structure=0	matches unstructured protein (random coil)
select turn	or	select structure=1	matches turns
select sheet	or	select structure=2	matches beta strands
select helix	or	select structure=3	includes all 3 types of helices
select dna	or	select structure=4	matches DNA
select rna	or	select structure=5	matches RNA
select carbohydrate	or	select structure=6	matches carbohydrates
select helix310	or	select substructure=7	matches 310 helices (DSSP code "G"). Example: 2JC9.pdb
select helixAlpha	or	select substructure=8	matches alpha helices (DSSP code "H")
select helixPi	or	select substructure=9	matches pi helices (DSSP code "I"). Example: 2JC9.pdb after calculate structure

Note: it is safe to use substructure for all selection commands. For ex., select substructure=2 selects beta strands, but select structure=8 selects nothing.

• color structure now applies different shades of color to alpha, 3₁₀ and pi helices, in addition to the classic coloring of helices, beta strands, turns and unstructured portions (see colors below).

• label %[substructure] labels with the texts: helixalpha, helix310, helixpi, sheet, turn, none

• structure helixAlpha ....
• structure helix310 ....
• structure helixPi ....

Reference section

• W. Kabsch, C. Sander (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637. doi:10.1002/bip.360221211
• DSSP Home Page: http://swift.cmbi.ru.nl/gv/dssp/

• M. Levitt, 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

• Codes for structure types:

	PDB code	SPSS code	Jmol codes substructure and name
right-handed alpha (default)	1	H	8 helixalpha █
right-handed omega	2
right-handed pi	3	G	7 helixpi █
right-handed gamma	4
right-handed 310	5	I	9 helix310 █
left-handed alpha	6
left-handed omega	7
left-handed gamma	8
27 ribbon/helix	9
polyproline	10
(beta) strand	0 first 1 parallel -1 antiparallel	E	2 sheet █
turn		T	1 turn █
isolated beta-bridge residue		B
bend		S
none (unstructured protein)		-	0 none █
DNA			4 dna █
RNA			5 rna █
carbohydrate			6 carbohydrate █
other*			-1 █

Helix types in PDB format: columns 39-40 of HELIX record, right-justified.

Strand sense in PDB format: columns 39-40 of SHEET record, right-justified.

(*) Other = not protein, not nucleic, not carbohydrate.

Pretty cartoons

Apply this script to get cartoons with a better-than-default look (it will take some more time to rotate them around):

set hermiteLevel -4; set ribbonAspectRatio 12;

or

set hermiteLevel 4; set ribbonAspectRatio 12;

which accelerates rotation (the thickness disappears while manipulating with the mouse)

This command is equivalent:

 set cartoonFancy on

See also Recycling_Corner#Improved_lighting

Loading part of the model

The use of load with the filter option allows that Jmol will only read some atoms from the file. This is useful e.g. to avoid the solvent molecules, to load a single chain, or to accelerate manipulation of large models (trace and cartoon may be rendered with just the Calpha atoms available)

See documentation (1, 2) and practical examples.

Nice display of membrane proteins

The Orientation of Proteins in Membranes (University of Michigan, Lomize Group) website holds a database with the (approximate) positions of proteins embedded in membranes. The two membrane (lipid bilayer) surfaces are displayed as a set of dummy atoms added to the pdb file, red (O) for the outer side and blue (N) for the inner side.

The following Jmol script locates those dummy atoms, removes them and inserts in their place the respective circular planes, making a cylinder to represent the portion of membrane where the protein is embedded. You can see the script at work at this page.

/* Code by Angel Herráez */
load "https://opm-assets.storage.googleapis.com/pdb/6xmt.pdb";
rotate X -90; /* +Z upwards, outer side */
define m~out [DUM].O; define m~in [DUM].N;
if ( {m~out}.size>0 ) {
  diam~mem = 2.2 * {m~out}.x.max; 
  z~out = {m~out}.xyz;
  if ( {m~in}.size>0 ) {
    z~in = {m~in}.xyz;
  } else { 
    z~in = - z~out; 
  }
} else if ( {m~in}.size>0 ) { 
  diam~mem = 2.2 * {m~in}.x.max; 
  z~in = {m~in}.xyz; 
  z~out = - z~in;
} else { 
  diam~mem = 52; 
  z~out = 14.9; 
  z~in = -14.9; 
};
draw surf~mem diameter @diam~mem color translucent navajoWhite cylinder @z~in @z~out fill;
draw surf~out scale @diam~mem color orangeRed arc @z~out @z~in;
draw surf~in scale @diam~mem color royalBlue arc @z~in @z~out;
delete [DUM]; 
select protein; cartoon only; color chain;

Contributors

AngelHerraez, Wayne Decatur, EricMartz, NicolasVervelle, Pimpim