Load aln - Revision history

Cchem: 2 revisions

2018-04-03T18:09:03Z

2 revisions

Speleo3: psico 3.3 drops needle dependency

2018-03-28T10:13:13Z

psico 3.3 drops needle dependency

Speleo3: created

2018-01-17T09:53:51Z

created

New page

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

[[load_aln]] loads a pairwise sequence alignment file as an alignment object into PyMOL.

== Installation ==

[[load_aln]] is available from the [[psico]] package and requires [http://biopython.org/ biopython] and [http://emboss.sourceforge.net/ needle (emboss)].

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 bioconda emboss
conda install biopython

== Usage ==

load_aln filename [, object [, mobile [, target
[, mobile_id [, target_id [, format [, transform ]]]]]]]

== Arguments ==

* '''filename''' = str: alignment file
* '''object''' = str: name of the object {default: filename prefix}
* '''mobile, target''' = str: atom selections {default: ids from alignment file}
* '''mobile_id, target_id''' = str: ids from alignment file {default: first two}
* '''format''' = str: file format, see http://biopython.org/wiki/AlignIO {default: guess from first line in file}
* '''transform''' = 0/1: superpose mobile on target (using [[fit]]) {default: 0}

== Example ==

Alignment file (alignment.faa):

>seq1
ACDEFG----HIKLMN
>seq2
ACNEYGGGGGHVRLMN

PyMOL script:

# create objects
fab ACDEFGHIKLMN, m1
fab ACNEYGGGGGHVRLMN, m2

# load alignment
import psico.importing
load_aln alignment.faa, mobile=m1, target=m2

# show sequence viewer
set seq_view

Use the alignment object to superpose with [[xfit]]:

import psico.fitting
xfit m1, m2, match=alignment, cycles=100
rebuild

== See Also ==

* [[align#Alignment Objects]]

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

← Older revision	Revision as of 18:09, 3 April 2018
(No difference)

@@ Line 7: / Line 7: @@
 == Installation ==
-[[load_aln]] is available from the [[psico]] package and requires [http://biopython.org/ biopython] and [http://emboss.sourceforge.net/ needle (emboss)].
+[[load_aln]] is available from the [[psico]] package and requires [http://biopython.org/ biopython].
-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 biopython