Difference between revisions of "Protein Community"

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(→‎Secondary structure)
(→‎Secondary structure)
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=== When reading files ===
 
=== 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 {{file|pdb}} or {{file|mmcif}} file contains HELIX/SHEET/TURN information''': that information is respected in '''all''' Jmol versions. In '''new''' Jmol versions, {{file|pdb}} and {{file|mmcif}} readers also read helix types alpha, pi, and 3<sub>10</sub>, and color them slightly differently ([http://jmol.sourceforge.net/jscolors/index.en.html#Secondary%20structure Jmol Colors]).
−
# '''If the PDB or mmCIF file des not contain HELIX/SHEET/TURN information''':  
+
# '''If the {{file|pdb}} or {{file|mmcif}} file des not contain HELIX/SHEET/TURN information''':  
 
#* '''Old''' versions of Jmol used Ramachandran-angle based calculation.  
 
#* '''Old''' versions of Jmol used Ramachandran-angle based calculation.  
 
#* '''New''' versions of Jmol use DSSP 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. [http://dx.doi.org/10.1016/0022-2836(77)90207-8 doi]
+
# In the case of '''alpha-carbon-only chains''', '''all''' versions of Jmol use the method of Levitt and Greer ([http://dx.doi.org/10.1016/0022-2836(77)90207-8 doi]).
−
# In '''new''' versions of Jmol the Ramachandran-angle-based calculation is still available (see below).
+
# In '''new''' versions of Jmol the calculation based on Ramachandran angles is still available (see below).
  
 
=== Forced recalculation of structure ===
 
=== Forced recalculation of structure ===
Line 36: Line 36:
 
=== Selection and coloring ===
 
=== Selection and coloring ===
  
−
* <code>color structure</code> now applies different shades of color to alpha, 3_10 and pi helices.
+
* <code>color structure</code> now applies different shades of color to alpha, 3<sub>10</sub> and pi helices ([http://jmol.sourceforge.net/jscolors/index.en.html#Secondary%20structure Jmol Colors]).
  
 
* <code>select helix</code> includes all 3 types of helices.
 
* <code>select helix</code> includes all 3 types of helices.
Line 42: Line 42:
 
* <code>select helix310</code> (example: 2JC9.pdb)
 
* <code>select helix310</code> (example: 2JC9.pdb)
 
* <code>select helixPi</code> (example: 2JC9.pdb)
 
* <code>select helixPi</code> (example: 2JC9.pdb)
−
* <code>select substructure=7</code> matches DSSP "G", i.e. 3_10 helices, same as <code>select helix310</code>  
+
* <code>select substructure=7</code> matches DSSP "G", i.e. 3<sub>10</sub> helices, same as <code>select helix310</code>  
 
* <code>select substructure=8</code> matches DSSP "H", i.e. alpha helices, same as <code>select helixAlpha</code>
 
* <code>select substructure=8</code> matches DSSP "H", i.e. alpha helices, same as <code>select helixAlpha</code>
 
* <code>select substructure=9</code> matches DSSP "I", i.e. pi helices, same as <code>select helixPi</code>
 
* <code>select substructure=9</code> matches DSSP "I", i.e. pi helices, same as <code>select helixPi</code>
 +
 
* <code>label %[substructure]</code> labels with the texts: helixalpha, helix310, helixpi, sheet, turn, none
 
* <code>label %[substructure]</code> labels with the texts: helixalpha, helix310, helixpi, sheet, turn, none
 +
 
* <code>structure helixAlpha</code> ....
 
* <code>structure helixAlpha</code> ....
 
* <code>structure helix310</code> ....
 
* <code>structure helix310</code> ....
Line 53: Line 55:
 
* 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
 
* 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
  
−
 
+
* Codes for structure types:
−
{| cellpadding="4" cellspacing="0" border="1"
+
{| cellpadding="4" cellspacing="0" border="1" style="margin-left:3ex;"
 
! !! PDB<br>code !! SPSS<br>code !! Jmol codes<br> substructure and name
 
! !! PDB<br>code !! SPSS<br>code !! Jmol codes<br> substructure and name
 
|-
 
|-
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| (beta) strand  || 0 first<br>1 parallel<br>-1 antiparallel || E || 2  sheet
 
| (beta) strand  || 0 first<br>1 parallel<br>-1 antiparallel || E || 2  sheet
 
|-
 
|-
−
| turn || || T || 1 turn  
+
| turn || || T || 1 turn  
 
|-
 
|-
 
| isolated beta-bridge residue || || B ||  
 
| isolated beta-bridge residue || || B ||  
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| bend || || S ||  
 
| bend || || S ||  
 
|-
 
|-
−
| none || || - || 0 none
+
| 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.
−
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.
−
Strand sense in PDB format: columns 39-40 of SHEET record, right-justified.
 

Revision as of 16:52, 16 October 2010

Jmol/JSmol Community

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.

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.

When reading files

  1. If the File icon.gifpdb or File icon.gifmmcif file contains HELIX/SHEET/TURN information: that information is respected in all Jmol versions. In new Jmol versions, File icon.gifpdb and File icon.gifmmcif readers also read helix types alpha, pi, and 310, and color them slightly differently (Jmol Colors).
  2. If the File icon.gifpdb or File icon.gifmmcif 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.

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.

Selection and coloring

  • color structure now applies different shades of color to alpha, 310 and pi helices (Jmol Colors).
  • select helix includes all 3 types of helices.
  • select helixAlpha
  • select helix310 (example: 2JC9.pdb)
  • select helixPi (example: 2JC9.pdb)
  • select substructure=7 matches DSSP "G", i.e. 310 helices, same as select helix310
  • select substructure=8 matches DSSP "H", i.e. alpha helices, same as select helixAlpha
  • select substructure=9 matches DSSP "I", i.e. pi helices, same as select helixPi
  • label %[substructure] labels with the texts: helixalpha, helix310, helixpi, sheet, turn, none
  • structure helixAlpha ....
  • structure helix310 ....
  • structure helixPi ....

Reference

  • 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
  • Codes for structure types:
PDB
code		 SPSS
code		 Jmol codes
substructure and name
right-handed alpha, 412 (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.

Contributors

AngelHerraez, Wayne Decatur, EricMartz, NicolasVervelle, Pimpim

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