Difference between revisions of "Protein Community"

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(secondary structure and DSSP)
(secondary structure and DSSP)
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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 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''':  
 
# '''If the PDB or 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.  
Line 24: Line 24:
 
* In '''old''' Jmol versions, calculated using the Ramachandran method.
 
* In '''old''' Jmol versions, calculated using the Ramachandran method.
 
* In '''new''' Jmol versions, calculated using the DSSP method.  
 
* In '''new''' Jmol versions, calculated using the DSSP method.  
−
==== New features in '''new''' Jmol versions ====
+
==== New commands ====
−
*<code>calculate structure ramachandran</code> is available for forcing the old method of calculation (it may have some advantages in certain contexts).
+
*<code>calculate structure ramachandran</code> is available for forcing the old method of calculation (it may have some advantages in certain contexts). It can be shortened to <code>calculate structure rama</code>.
 
* <code>calculate hBonds structure</code> does DSSP determining hydrogen bonds only.
 
* <code>calculate hBonds structure</code> does DSSP determining hydrogen bonds only.
−
* <code>save structure s1</code> (for example) saves the PDB authors' structure assignment with the internal ID 's1' for later restoring.
+
* <code>set defaultStructureDSSP false</code> will change the defaults of file load and <code>calculate structure</code> to use the Ramachandran method; by default, it is ''true'' and uses the DSSP method.
 +
* <code>set dsspCalculateHydrogenAlways false</code> 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.
 +
* <code>show dssp</code> displays a report of the DSSP calculation.
 +
* <code>set debug</code> displays a verbose DSSP calculation.
 +
* <code>save structure s1</code> (for example) saves in memory the current structure assignment with the internal ID 's1' for later restoring.
 
* <code>restore structure s1</code> restores the previously saved assignment.
 
* <code>restore structure s1</code> restores the previously saved assignment.
−
* <code>color structure</code> now applies different shades of color to alpha, 3(10) and pi helixes.
 
−
* <code>show DSSP</code> displays a report of the DSSP calculation.
 
−
* <code>set DEBUG</code>displays a verbose DSSP calculation.
 
−
* <code>set defaultStructureDSSP false</code> (by default, it is ''true'') will change the defaults of file load and <code>calculate structure</code> to use the Ramachandran method instead of the DSSP method.
 
−
* <code>set dsspCalculateHydrogenAlways false</code> 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.
 
−
* select helix
 
−
* select helixalpha
 
−
* select helix310
 
−
* select helixpi
 
−
          # try this with 2JC9 for a DSSP >>555<< run
 
−
  select substructure = 7 # DSSP "G" -- 3/10 helices
 
−
  select substructure = 8 # DSSP "H" -- alpha helices
 
−
  select substructure = 9 # DSSP "I" -- pi helices
 
  
−
  label {*.ca} %[substructure]
+
=== Selection and coloring ===
  
−
  STRUCTURE HELIXALPHA ....
+
* <code>color structure</code> now applies different shades of color to alpha, 3_10 and pi helices.
−
  STRUCTURE HELIX310 ....
 
−
  STRUCTURE HELIXPI ....
 
  
−
See http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm for examples.
+
* <code>select helix</code> includes all 3 types of helices.
 +
* <code>select helixAlpha</code>
 +
* <code>select helix310</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=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>label %[substructure]</code> labels with the texts: helixalpha, helix310, helixpi, sheet, turn, none
 +
* <code>STRUCTURE HELIXALPHA</code> ....
 +
* <code>STRUCTURE HELIX310</code> ....
 +
* <code>STRUCTURE HELIXPI</code> ....

Revision as of 11:59, 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 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.
  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 Ramachandran-angle-based calculation 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, 3_10 and pi helices.
  • 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. 3_10 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 ....

Contributors

AngelHerraez, Wayne Decatur, EricMartz, NicolasVervelle, Pimpim

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