https://pymolwiki.org/index.php?title=Load_aln&feed=atom&action=history
Load aln - Revision history
2024-03-29T13:42:11Z
Revision history for this page on the wiki
MediaWiki 1.35.7
https://pymolwiki.org/index.php?title=Load_aln&diff=12741&oldid=prev
Speleo3: psico 3.3 drops needle dependency
2018-03-28T10:13:13Z
<p>psico 3.3 drops needle dependency</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 10:13, 28 March 2018</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7" >Line 7:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Installation ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Installation ==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[load_aln]] is available from the [[psico]] package and requires [http://biopython.org/ biopython<del class="diffchange diffchange-inline">] and [http://emboss.sourceforge.net/ needle (emboss)</del>].</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[load_aln]] is available from the [[psico]] package and requires [http://biopython.org/ biopython].</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">For Linux and MacOS, all </del>dependencies are available from [https://anaconda.org Anaconda Cloud]:</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">All </ins>dependencies are available from [https://anaconda.org Anaconda Cloud]:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> conda install -c schrodinger pymol</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> conda install -c schrodinger pymol</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> conda install -c schrodinger pymol-psico</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> conda install -c schrodinger pymol-psico</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;"> conda install -c bioconda emboss</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> conda install biopython</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> conda install biopython</div></td></tr>
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Speleo3
https://pymolwiki.org/index.php?title=Load_aln&diff=12718&oldid=prev
Speleo3: created
2018-01-17T09:53:51Z
<p>created</p>
<p><b>New page</b></p><div>{{Infobox psico<br />
|module = psico.importing<br />
}}<br />
<br />
[[load_aln]] loads a pairwise sequence alignment file as an alignment object into PyMOL.<br />
<br />
== Installation ==<br />
<br />
[[load_aln]] is available from the [[psico]] package and requires [http://biopython.org/ biopython] and [http://emboss.sourceforge.net/ needle (emboss)].<br />
<br />
For Linux and MacOS, all dependencies are available from [https://anaconda.org Anaconda Cloud]:<br />
<br />
conda install -c schrodinger pymol<br />
conda install -c schrodinger pymol-psico<br />
conda install -c bioconda emboss<br />
conda install biopython<br />
<br />
== Usage ==<br />
<br />
load_aln filename [, object [, mobile [, target<br />
[, mobile_id [, target_id [, format [, transform ]]]]]]]<br />
<br />
== Arguments ==<br />
<br />
* '''filename''' = str: alignment file<br />
* '''object''' = str: name of the object {default: filename prefix}<br />
* '''mobile, target''' = str: atom selections {default: ids from alignment file}<br />
* '''mobile_id, target_id''' = str: ids from alignment file {default: first two}<br />
* '''format''' = str: file format, see http://biopython.org/wiki/AlignIO {default: guess from first line in file}<br />
* '''transform''' = 0/1: superpose mobile on target (using [[fit]]) {default: 0}<br />
<br />
== Example ==<br />
<br />
Alignment file (alignment.faa):<br />
<br />
>seq1<br />
ACDEFG----HIKLMN<br />
>seq2<br />
ACNEYGGGGGHVRLMN<br />
<br />
PyMOL script:<br />
<br />
# create objects<br />
fab ACDEFGHIKLMN, m1<br />
fab ACNEYGGGGGHVRLMN, m2<br />
<br />
# load alignment<br />
import psico.importing<br />
load_aln alignment.faa, mobile=m1, target=m2<br />
<br />
# show sequence viewer<br />
set seq_view<br />
<br />
Use the alignment object to superpose with [[xfit]]:<br />
<br />
import psico.fitting<br />
xfit m1, m2, match=alignment, cycles=100<br />
rebuild<br />
<br />
== See Also ==<br />
<br />
* [[align#Alignment Objects]]<br />
<br />
[[Category:Script Library]]<br />
[[Category:Structural_Biology_Scripts]]</div>
Speleo3