Difference between revisions of "Protein Community"

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(secondary structure and DSSP)
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{{Jmol Community Sections}}
 
{{Jmol Community Sections}}
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=== Protein 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.
 
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.
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* [[User:EricMartz|Eric Martz]]: [http://bioinformatics.org/firstglance 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 [http://www.molslides.org/ MolSlides.Org]
 
* [[User:EricMartz|Eric Martz]]: [http://bioinformatics.org/firstglance 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 [http://www.molslides.org/ MolSlides.Org]
  
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Molecular surfaces in Jmol: [http://biomodel.uah.es/Jmol/surfaces/ documentation and testing page]
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== Molecular surfaces ==
 +
[http://biomodel.uah.es/Jmol/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 ===
 +
# '''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''':
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#* '''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. [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).
 +
 
 +
=== Forced recalculation of structure ===
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==== <code>calculate structure</code>  ====
 +
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 features in '''new''' Jmol versions ====
 +
*<code>calculate structure ramachandran</code> is available for forcing the old method of calculation (it may have some advantages in certain contexts).
 +
* <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.
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* <code>restore structure s1</code> restores the previously saved assignment.
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* <code>color structure</code> now applies different shades of color to alpha, 3(10) and pi helixes.
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* <code>show DSSP</code> displays a report of the DSSP calculation.
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* <code>set DEBUG</code>displays a verbose DSSP calculation.
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* <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.
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* select helix
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* select helixalpha
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* select helix310
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* select helixpi
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          # try this with 2JC9 for a DSSP >>555<< run
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  select substructure = 7 # DSSP "G" -- 3/10 helices
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  select substructure = 8 # DSSP "H" -- alpha helices
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  select substructure = 9 # DSSP "I" -- pi helices
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  label {*.ca} %[substructure]
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 +
  STRUCTURE HELIXALPHA ....
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  STRUCTURE HELIX310 ....
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  STRUCTURE HELIXPI ....
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 +
See http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm for examples.

Revision as of 11:17, 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 features in new Jmol versions

  • calculate structure ramachandran is available for forcing the old method of calculation (it may have some advantages in certain contexts).
  • calculate hBonds structure does DSSP determining hydrogen bonds only.
  • save structure s1 (for example) saves the PDB authors' structure assignment with the internal ID 's1' for later restoring.
  • restore structure s1 restores the previously saved assignment.
  • color structure now applies different shades of color to alpha, 3(10) and pi helixes.
  • show DSSP displays a report of the DSSP calculation.
  • set DEBUGdisplays a verbose DSSP calculation.
  • set defaultStructureDSSP false (by default, it is true) will change the defaults of file load and calculate structure to use the Ramachandran method instead of 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.
  • 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]

  STRUCTURE HELIXALPHA ....   STRUCTURE HELIX310 ....   STRUCTURE HELIXPI ....

See http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm for examples.

Contributors

AngelHerraez, Wayne Decatur, EricMartz, NicolasVervelle, Pimpim

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