Load aln

Included in psico This command or function is available from psico, which is a PyMOL extension.
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 biopython and needle (emboss).

For Linux and MacOS, all dependencies are available from 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