Msms surface - Revision history

Cchem: 2 revisions

2017-11-13T03:27:11Z

2 revisions

Speleo3: -c speleo3

2017-10-17T18:38:43Z

-c speleo3

Speleo3: created

2017-10-17T10:15:31Z

created

New page

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

[[msms_surface]] calculates a molecular surface with [http://mgltools.scripps.edu/packages/MSMS MSMS] and loads it into PyMOL as a CGO.

== Installation ==

[[msms_surface]] is available from the [[psico]] package and requires the [http://mgltools.scripps.edu/downloads#msms msms] binary.

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

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c bioconda msms

== Usage ==

msms_surface [ selection [, state [, density [, name
[, atomcolors [, exe [, preserve ]]]]]]]

== Arguments ==

* '''selection''' = str: atom selection {default: polymer}
* '''state''' = int: object state {default: 1}
* '''density''' = float: MSMS surface point density {default: 3}
* '''name''' = str: name of CGO object to create
* '''atomcolors''' = 0/1: color surface by atom colors {default: 0}
* '''exe''' = str: path to msms binary {default: find in $PATH}
* '''preserve''' = 0/1: don't delete msms generated files {default: 0}

== Examples ==

Use atom colors:

import psico.msms
fetch 1ubq, async=0
msms_surface atomcolors=1

Use a solid color:

msms_surface name=bluesurf
color blue, bluesurf

== See Also ==

* [[MSMS]] (plugin with GUI)
* [[surface]]

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

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

@@ Line 9: / Line 9: @@
 [[msms_surface]] is available from the [[psico]] package and requires the [http://mgltools.scripps.edu/downloads#msms msms] binary.
-For Linux, 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 bioconda msms
+  conda install -c bioconda -c speleo3 msms
 == Usage ==