Dssp - Revision history

Cchem: 2 revisions

2017-11-13T03:27:11Z

2 revisions

Speleo3: -c speleo3

2017-10-17T18:57:08Z

-c speleo3

Speleo3: created

2017-10-17T12:14:12Z

created

New page

{{Infobox psico
|module = psico.editing
}}

[[dssp]] is a wrapper for the popular [http://swift.cmbi.ru.nl/gv/dssp/ DSSP] program, which computes secondary structure. The command updates PyMOL's '''ss''' atom property.

== Installation ==

The [[dssp]] command is available from the [[psico]] package and requires the [http://swift.cmbi.ru.nl/gv/dssp/ dssp] binary (or mkdssp, dsspcmbi, dssp-2).

For Linux and macOS, all dependencies are available from [https://anaconda.org Anaconda Cloud]:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c salilab dssp

== Usage ==

dssp [ selection [, exe [, raw [, state ]]]]

== Arguments ==

* '''selection''' = str: atom selection {default: all}
* '''exe''' = str: path to dssp binary {default: search $PATH for dsspcmbi, dssp, dssp-2, mkdssp}
* '''raw''' = str: [[iterate#Exposed_Variables|atom property]] to assign the dssp secondary structure type to. This type will also be translated to PyMOL's H/S/L types and assiged to the '''ss''' property {default: }
* '''state''' = int: object state {default: -1 (current state)}

== Example ==

import psico.editing
fetch 1ubq, async=0

dssp all, raw=custom

color gray
color red, custom H
color orange, custom G
color yellow, custom E
color wheat, custom B
color forest, custom T
color green, custom S
set cartoon_discrete_colors, 1

== See Also ==

* [[DSSP Stride]] (plugin with GUI)
* [[dss]]

[[Category:Script Library]]
[[Category:Structural_Biology_Scripts]]

← Older revision	Revision as of 03:27, 13 November 2017
(No difference)

@@ Line 9: / Line 9: @@
 The [[dssp]] command is available from the [[psico]] package and requires the [http://swift.cmbi.ru.nl/gv/dssp/ dssp] binary (or mkdssp, dsspcmbi, dssp-2).
-For Linux and macOS, all dependencies are available from [https://anaconda.org Anaconda Cloud]:
+All dependencies are available from [https://anaconda.org Anaconda Cloud]:
   conda install -c schrodinger pymol
   conda install -c schrodinger pymol-psico
-  conda install -c salilab dssp
+  conda install -c salilab -c speleo3 dssp
 == Usage ==