Load aln
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Included in psico | |
Module | psico.importing |
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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