Author: bugman
Date: Wed Feb 4 19:29:00 2015
New Revision: 27533
URL: http://svn.gna.org/viewcvs/relax?rev=27533&view=rev
Log:
Set up a redirect for the structure.align user function to
structure.superimpose.
Modified:
website/.setup_redirects.py
website/manual/structure_align.html
Modified: website/.setup_redirects.py
URL:
http://svn.gna.org/viewcvs/relax/website/.setup_redirects.py?rev=27533&r1=27532&r2=27533&view=diff
==============================================================================
--- website/.setup_redirects.py (original)
+++ website/.setup_redirects.py Wed Feb 4 19:29:00 2015
@@ -122,6 +122,7 @@
['manual/relax_fit_mean_and_error.html',
'%s/manual/spectrum_error_analysis.html'%url],
['manual/relax_fit_read.html',
'%s/manual/spectrum_read_intensities.html'%url],
['manual/structure_vectors.html',
'%s/manual/interatom_unit_vectors.html'%url],
+ ['manual/structure_align.html',
'%s/manual/structure_superimpose.html'%url],
['manual/temperature.html',
'%s/manual/spectrometer_temperature.html'%url]
]
Modified: website/manual/structure_align.html
URL:
http://svn.gna.org/viewcvs/relax/website/manual/structure_align.html?rev=27533&r1=27532&r2=27533&view=diff
==============================================================================
--- website/manual/structure_align.html (original)
+++ website/manual/structure_align.html Wed Feb 4 19:29:00 2015
@@ -1,304 +1,6 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.1//EN">
-
-<!--Converted with LaTeX2HTML 2008 (1.71)
-original version by: Nikos Drakos, CBLU, University of Leeds
-* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
-* with significant contributions from:
- Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML>
<HEAD>
-<TITLE>structure.align</TITLE>
-<META NAME="description" CONTENT="structure.align">
-<META NAME="keywords" CONTENT="relax">
-<META NAME="resource-type" CONTENT="document">
-<META NAME="distribution" CONTENT="global">
-
-<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=utf-8">
-
- <!--Google analytics JS-->
- <script type="text/javascript">
-
- var _gaq = _gaq || [];
- _gaq.push(['_setAccount', 'UA-30096326-1']);
- _gaq.push(['_setDomainName', 'nmr-relax.com']);
- _gaq.push(['_trackPageview']);
-
- (function() {
- var ga = document.createElement('script'); ga.type =
'text/javascript'; ga.async = true;
- ga.src = ('https:' == document.location.protocol ? 'https://ssl' :
'http://www') + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0];
s.parentNode.insertBefore(ga, s);
- })();
-
- </script>
-
-<LINK REL="STYLESHEET" HREF="relax.css">
-
-<LINK REL="next" HREF="structure_atomic_fluctuations.html">
-<LINK REL="previous" HREF="structure_add_model.html">
-<LINK REL="up" HREF="The_list_of_functions.html">
-<LINK REL="next" HREF="structure_atomic_fluctuations.html">
+ <meta http-equiv="refresh" content="0;
url=http://www.nmr-relax.com/manual/structure_superimpose.html";>
</HEAD>
-
-<BODY >
-
-<DIV CLASS="navigation"><!--Navigation Panel-->
-<A NAME="tex2html20499"
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SRC="up.png"></A>
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ALT="index" SRC="index.png"></A> <A NAME="tex2html1"
- HREF="http://download.gna.org/relax/manual/relax.pdf";><IMG
- ALIGN="BOTTOM" BORDER="0"
SRC="http://www.nmr-relax.com/images/pdf_icon_nav.png";
- ALT="pdf_icon_nav.png"></A><A NAME="tex2html2"
- HREF="http://www.nmr-relax.com";><IMG
- ALIGN="BOTTOM" BORDER="0"
SRC="http://www.nmr-relax.com/images/relax_logo_nav.png";
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-<B> Up:</B> <A NAME="tex2html20494"
- HREF="The_list_of_functions.html">The list of functions</A>
-<B> Previous:</B> <A NAME="tex2html20488"
- HREF="structure_add_model.html">structure.add_model</A>
- <B> <A NAME="tex2html20496"
- HREF="Contents.html">Contents</A></B>
- <B> <A NAME="tex2html20498"
- HREF="Index.html">Index</A></B>
-<BR>
-<BR></DIV>
-<!--End of Navigation Panel-->
-<!--Table of Child-Links-->
-<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
-
-<UL CLASS="ChildLinks">
-<LI><A NAME="tex2html20501"
- HREF="structure_align.html#SECTION0812229100000000000000">Synopsis</A>
-<LI><A NAME="tex2html20502"
- HREF="structure_align.html#SECTION0812229200000000000000">Defaults</A>
-<LI><A NAME="tex2html20503"
- HREF="structure_align.html#SECTION0812229300000000000000">Keyword
arguments</A>
-<LI><A NAME="tex2html20504"
- HREF="structure_align.html#SECTION0812229400000000000000">Description</A>
-<LI><A NAME="tex2html20505"
- HREF="structure_align.html#SECTION0812229500000000000000">Prompt
examples</A>
-</UL>
-<!--End of Table of Child-Links-->
-<HR>
-
-<H2><A NAME="SECTION0812229000000000000000"></A> <A
NAME="uf:_structure.align"></A>
-<BR>
-structure.align
-</H2>
-<IMG
- WIDTH="128" HEIGHT="128" ALIGN="BOTTOM" BORDER="0"
- SRC="./structure.png"
- ALT="Image structure">
-
-<P>
-
-<H3><A NAME="SECTION0812229100000000000000">
-Synopsis</A>
-</H3>
-
-<P>
-Align and superimpose different structures.
-
-<P>
-
-<H3><A NAME="SECTION0812229200000000000000">
-Defaults</A>
-</H3>
-
-<P>
-<DIV ALIGN="LEFT">
-<SPAN CLASS="textsf"><SPAN
CLASS="textbf">structure.align</SPAN>(pipes=None, models=None,
molecules=None, atom_id=None, displace_id=None, method=`fit to mean',
matrix=`BLOSUM62', gap_open_penalty=10.0, gap_extend_penalty=1.0,
end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0, centre_type=`centroid',
centroid=None)</SPAN>
-
-</DIV>
-
-<P>
-
-<H3><A NAME="SECTION0812229300000000000000">
-Keyword arguments</A>
-</H3>
-
-<P>
- <SPAN CLASS="textsf">pipes:</SPAN> The data pipes to use in the alignment
and superimposition.
-
-<P>
- <SPAN CLASS="textsf">models:</SPAN> The list of models for each data pipe
to use in the alignment and superimposition. The number of elements must
match the pipes argument. If no models are given, then all will be used.
-
-<P>
- <SPAN CLASS="textsf">molecules:</SPAN> The list of molecules<A
NAME="39617"></A> for each data pipe to use in the alignment and
superimposition. This allows differently named molecules<A NAME="39618"></A>
in the same or different data pipes to be superimposed. The number of
elements must match the pipes argument. If no molecules<A NAME="39619"></A>
are given, then all will be used.
-
-<P>
- <SPAN CLASS="textsf">atom_id:</SPAN> The atom identification string of
the coordinates of interest.
-
-<P>
- <SPAN CLASS="textsf">displace_id:</SPAN> The atom identification string
for restricting the displacement to a subset of all atoms. If not set, then
all atoms will be translated and rotated. If supplied as a list of IDs, then
the number of items must match the number of structures.
-
-<P>
- <SPAN CLASS="textsf">method:</SPAN> The superimposition method.
-
-<P>
- <SPAN CLASS="textsf">matrix:</SPAN> The substitution matrix to use in the
pairwise sequence<A NAME="39628"></A> alignment algorithm.
-
-<P>
- <SPAN CLASS="textsf">gap_open_penalty:</SPAN> The penalty for introducing
gaps, as a positive number.
-
-<P>
- <SPAN CLASS="textsf">gap_extend_penalty:</SPAN> The penalty for extending
a gap, as a positive number.
-
-<P>
- <SPAN CLASS="textsf">end_gap_open_penalty:</SPAN> The optional penalty
for opening a gap at the end of a sequence.<A NAME="39635"></A>
-
-<P>
- <SPAN CLASS="textsf">end_gap_extend_penalty:</SPAN> The optional penalty
for extending a gap at the end of a sequence.<A NAME="39638"></A>
-
-<P>
- <SPAN CLASS="textsf">centre_type:</SPAN> The type of centre to user for
the superimposition, <SPAN CLASS="MATH"><I>i</I></SPAN>.e. either the
standard centroid superimposition or a superimposition using the centre of
mass (CoM).
-
-<P>
- <SPAN CLASS="textsf">centroid:</SPAN> The alternative position of the
centroid.
-
-<P>
-
-<H3><A NAME="SECTION0812229400000000000000">
-Description</A>
-</H3>
-
-<P>
-This allows a set of related structures to be superimposed to each other.
The current algorithm will only use atoms with the same residue name and
number and atom name in the superimposition, hence this is not a true
sequence<A NAME="39644"></A> alignment. Just as with the
structure.superimpose user function two methods are currently supported:
-
-<P>
-<DL>
-<DT><STRONG>`<TT>fit to mean</TT>' -</STRONG></DT>
-<DD>All models are fit to the mean structure. This is the default and most
accurate method for an ensemble description. It is an iterative method which
first calculates a mean structure and then fits each model to the mean
structure using the Kabsch algorithm. This is repeated until convergence.
-
-</DD>
-<DT><STRONG>`<TT>fit to first</TT>' -</STRONG></DT>
-<DD>This is quicker but is not as accurate for an ensemble description. The
Kabsch algorithm is used to rotate and translate each model to be
superimposed onto the first model of the first data pipe.
-</DD>
-</DL>
-
-<P>
-Support for multiple structures is provided by the data pipes, model numbers
and molecule<A NAME="39649"></A> names arguments. Each data pipe, model and
molecule<A NAME="39650"></A> combination will be treated as a separate
structure. As only atomic coordinates with the same residue name and number
and atom name will be assembled, structures with slightly different atomic
structures can be compared. If the list of models is not supplied, then all
models of all data pipes will be used. If the optional molecules<A
NAME="39651"></A> list is supplied, each molecule<A NAME="39652"></A> in the
list will be considered as a separate structure for comparison between each
other.
-
-<P>
-The atom ID string, which uses the same notation as the spin ID, can be used
to restrict the coordinates compared to a subset of molecules,<A
NAME="39653"></A> residues, or atoms. For example to only use backbone heavy
atoms in a protein, set the atom ID to `<TT>@N,C,CA,O</TT>', assuming those
are the names of the atoms in the 3D structural file.
-
-<P>
-The displacement ID string, which is similar to the atom ID, gives finer
control over which atoms are translated and rotated by the algorithm. When
not set this allows, for example, to align structures based on a set of
backbone heavy atoms and the backbone protons and side-chains are displaced
by default. Or if set to the same as the atom ID, if a single domain is
aligned, then just that domain will be displaced.
-
-<P>
-To find common atoms between diverse structures, a sequence<A
NAME="39655"></A> alignment is performed between the molecules.<A
NAME="39656"></A> This will be a pairwise alignment of each structure to the
first. The Needleman-Wunsch algorithm (NW70), modified to use the logic of
the EMBOSS software for handling gap opening and extension penalties, as well
as end penalties, will be used. The substitution matrix can be one of
BLOSUM62 or PAM250 for proteins, or NUC 4.4 for DNA/RNA.
-
-<P>
-By supplying the position of the centroid, an alternative position than the
standard rigid body centre is used as the focal point of the superimposition.
The allows, for example, the superimposition about a pivot point.
-
-<P>
-
-<H3><A NAME="SECTION0812229500000000000000">
-Prompt examples</A>
-</H3>
-
-<P>
-To superimpose all sets of models, exactly as in the structure.superimpose
user function, type one of:
-
-<P>
-<PRE>[numbers=none]
-relax> structure.align()
-</PRE>
-
-<P>
-<PRE>[numbers=none]
-relax> structure.align(method='fit to mean')
-</PRE>
-
-<P>
-To superimpose the models 1, 2, 3, 5 onto model 4, type:
-
-<P>
-<PRE>[numbers=none]
-relax> structure.align(models=[[4, 1, 2, 3, 5]], method='fit to first')
-</PRE>
-
-<P>
-To superimpose an ensemble of protein structures using only the backbone
heavy atoms, type one of:
-
-<P>
-<PRE>[numbers=none]
-relax> structure.align(atom_id='@N,C,CA,O')
-</PRE>
-
-<P>
-<PRE>[numbers=none]
-relax> structure.align(method='fit to mean', atom_id='@N,C,CA,O')
-</PRE>
-
-<P>
-To superimpose the structures in the `<TT>A</TT>' data pipe onto the
structures of the `<TT>B</TT>' data pipe using backbone heavy atoms, type one
of:
-
-<P>
-<PRE>[numbers=none]
-relax> structure.align(['B', 'A'], None, 'fit to first', '@N,C,CA,O')
-</PRE>
-
-<P>
-<PRE>[numbers=none]
-relax> structure.align(pipes=['B', 'A'], method='fit to first',
atom_id='@N,C,CA,O')
-</PRE>
-
-<P>
-
-<BR>
-
-<DIV CLASS="navigation"><HR>
-<!--Navigation Panel-->
-<A NAME="tex2html20499"
- HREF="structure_atomic_fluctuations.html">
-<IMG WIDTH="48" HEIGHT="48" TITLE="Next" ALIGN="BOTTOM" BORDER="0"
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-<B> Previous:</B> <A NAME="tex2html20488"
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- <B> <A NAME="tex2html20496"
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- <B> <A NAME="tex2html20498"
- HREF="Index.html">Index</A></B> </DIV>
-<!--End of Navigation Panel-->
-<ADDRESS>
-The <a href="http://www.nmr-relax.com";>relax</a> <a
href="http://www.nmr-relax.com/manual/";>user manual</a> (<a
href="http://download.gna.org/relax/manual/relax.pdf";>PDF</a>), created
2015-01-27.
-</ADDRESS>
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</HTML>
r27533 - in /website: .setup_redirects.py manual/structure_align.html![http://www.nmr-relax.com/images/pdf_icon_nav.png"](/images/pdf_icon_nav.png"){kind=link}
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