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The Biopython Structural Bioinformatics FAQ
Bio.PDB is a biopython module that focuses on working with crystal structures of biological macromolecules. This document gives a fairly complete overview of Bio.PDB.
Bio.PDB's installation
Bio.PDB is automatically installed as part of Biopython. Biopython can be obtained from http://www.biopython.org. It runs on many platforms (Linux/Unix, windows, Mac,...).
Who's using Bio.PDB?
Bio.PDB was used in the construction of DISEMBL, a web server that predicts disordered regions in proteins (http://dis.embl.de/), and COLUMBA, a website that provides annotated protein structures (http://www.columba-db.de/). Bio.PDB has also been used to perform a large scale search for active sites similarities between protein structures in the PDB (see [http://dx.doi.org/10.1002/prot.10338 \textit{Proteins Struct. Func. Gen., \textbf{2003, 51, 96-108]) , and to develop a new algorithm that identifies linear secondary structure elements ([\emph{BMC Bioinformatics, \textbf{2005, 6, 202 http://www.biomedcentral.com/1471-2105/6/202]).
Judging from requests for features and information, Bio.PDB is also used by several LPCs (Large Pharmaceutical Companies :-).
Is there a Bio.PDB reference?
Yes, and I'd appreciate it if you would refer to Bio.PDB in publications if you make use of it. The reference is:
\begin{quote Hamelryck, T., Manderick, B. (2003) PDB parser and structure class implemented in Python. \textit{Bioinformatics, \textbf{19, 2308-2310. \end{quote The article can be freely downloaded via the Bioinformatics journal website (http://www.binf.ku.dk/users/thamelry/references.html). I welcome e-mails telling me what you are using Bio.PDB for. Feature requests are welcome too.
How well tested is Bio.PDB?
Pretty well, actually. Bio.PDB has been extensively tested on nearly 5500 structures from the PDB - all structures seemed to be parsed correctly. More details can be found in the Bio.PDB Bioinformatics article. Bio.PDB has been used/is being used in many research projects as a reliable tool. In fact, I'm using Bio.PDB almost daily for research purposes and continue working on improving it and adding new features.
How fast is it?
The PDBParser
performance was tested on about 800 structures
(each belonging to a unique SCOP superfamily). This takes about 20
minutes, or on average 1.5 seconds per structure. Parsing the structure
of the large ribosomal subunit (1FKK), which contains about 64000
atoms, takes 10 seconds on a 1000 MHz PC. In short: it's more than
fast enough for many applications.
Why should I use Bio.PDB?
Bio.PDB might be exactly what you want, and then again it might not. If you are interested in data mining the PDB header, you might want to look elsewhere because there is only limited support for this. If you look for a powerful, complete data structure to access the atomic data Bio.PDB is probably for you.
General questions
Importing Bio.PDB
That's simple:
from Bio.PDB import *
Is there support for molecular graphics?
Not directly, mostly since there are quite a few Python based/Python aware solutions already, that can potentially be used with Bio.PDB. My choice is Pymol, BTW (I've used this successfully with Bio.PDB, and there will probably be specific PyMol modules in Bio.PDB soon/some day). Python based/aware molecular graphics solutions include:
- PyMol: http://pymol.sourceforge.net/
- Chimera: http://www.cgl.ucsf.edu/chimera/
- PMV: http://www.scripps.edu/ sanner/python/
- Coot: http://www.ysbl.york.ac.uk/ emsley/coot/
- CCP4mg: http://www.ysbl.york.ac.uk/ lizp/molgraphics.html
- mmLib: http://pymmlib.sourceforge.net/
- VMD: http://www.ks.uiuc.edu/Research/vmd/
- MMTK: http://starship.python.net/crew/hinsen/MMTK/
I'd be crazy to write another molecular graphics application (been there - done that, actually :-).
How do I create a structure object from a PDB file?
First, create a PDBParser
parser = PDBParser()
Then, create a structure object from a PDB file in the following way (the PDB file in this case is called '1FAT.pdb', 'PHA-L' is a user defined name for the structure):
structure = parser.get_structure('PHA-L', '1FAT.pdb')
How do I create a structure object from an mmCIF file?
Similarly to the case the case of PDB files, first create an MMCIFParser
parser = MMCIFParser()
Then use this parser to create a structure object from the mmCIF file:
structure = parser.get_structure('PHA-L', '1FAT.cif')
...and what about the new PDB XML format?
That's not yet supported, but I'm definitely planning to support that in the future (it's not a lot of work). Contact me if you need this, it might encourage me :-).
I'd like to have some more low level access to an mmCIF file...
You got it. You can create a python dictionary that maps all mmCIF
tags in an mmCIF file to their values. If there are multiple values
(like in the case of tag _atom_site.Cartn_y
, which holds
the y coordinates of all atoms), the tag is mapped to a list of values.
The dictionary is created from the mmCIF file as follows:
mmcif_dict = MMCIF2Dict('1FAT.cif')
Example: get the solvent content from an mmCIF file:
sc = mmcif_dict['_exptl_crystal.density_percent_sol']
Example: get the list of the y coordinates of all atoms
y_list = mmcif_dict['_atom_site.Cartn_y']
Can I access the header information?
Thanks to Christian Rother you can access some information from the
PDB header. Note however that many PDB files contain headers with
incomplete or erroneous information. Many of the errors have been
fixed in the equivalent mmCIF files.
Hence, if you are interested in the header information, it is a good idea to extract information from mmCIF files using the MMCIF2Dict
tool described above, instead of parsing the PDB header.
Now that is clarified, let's return to parsing the PDB header. The
structure object has an attribute called header
which is
a python dictionary that maps header records to their values.
resolution = structure.header['resolution'] keywords = structure.header['keywords']
The available keys are name
, head
, deposition_date
, release_date
, resolution
, structure_reference
(maps to
a list of references), journal_reference
, author
(maps to a dictionary with various information about
the crystallized compound).
The dictionary can also be created without creating a Structure
object, ie. directly from the PDB file:
handle = open(filename,'r') header_dict = parse_pdb_header(handle) handle.close()
Can I use Bio.PDB with NMR structures (ie. with more than one model)?
Sure. Many PDB parsers assume that there is only one model, making
them all but useless for NMR structures. The design of the Structure
object makes it easy to handle PDB files with more than one model
(see section #The Structure object).
How do I download structures from the PDB?
This can be done using the PDBList
object, using the retrieve_pdb_file
method. The argument for this method is the PDB identifier of the
pdbl = PDBList() pdbl.retrieve_pdb_file('1FAT')
The PDBList
class can also be used as a command-line tool:
python PDBList.py 1fat
The downloaded file will be called pdb1fat.ent
and stored
in the current working directory. Note that the retrieve_pdb_file
method also has an optional argument pdir
that specifies
a specific directory in which to store the downloaded PDB files.
The retrieve_pdb_file
method also has some options for specifying
the compression format used for the download, and the program used
for local decompression (default .Z
format and gunzip
In addition, the PDB ftp site can be specified upon creation of the
object. By default, the server of the Worldwide Protein Data Bank (\url{ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/})
is used. See the API documentation for more details. Thanks again
to Kristian Rother for donating this module.
How do I download the entire PDB?
The following commands will store all PDB files in the /data/pdb
python PDBList.py all /data/pdb
python PDBList.py all /data/pdb -d
The API method for this is called download_entire_pdb
Adding the -d
option will store all files in the same directory.
Otherwise, they are sorted into PDB-style subdirectories according
to their PDB ID's. Depending on the traffic, a complete download will
take 2-4 days.
How do I keep a local copy of the PDB up-to-date?
This can also be done using the PDBList
object. One simply
creates a PDBList
object (specifying the directory where
the local copy of the PDB is present) and calls the update_pdb
pl = PDBList(pdb='/data/pdb') pl.update_pdb()
One can of course make a weekly cronjob out of this to keep the local copy automatically up-to-date. The PDB ftp site can also be specified (see API documentation).
has some additional methods that can be of use. The
method can be used to get a list of all
obsolete PDB entries. The changed_this_week
method can
be used to obtain the entries that were added, modified or obsoleted
during the current week. For more info on the possibilities of PDBList
see the API documentation.
What about all those buggy PDB files?
It is well known that many PDB files contain semantic errors (I'm not talking about the structures themselves know, but their representation in PDB files). Bio.PDB tries to handle this in two ways. The PDBParser object can behave in two ways: a restrictive way and a permissive way (THIS IS NOW THE DEFAULT). The restrictive way used to be the default, but people seemed to think that Bio.PDB 'crashed' due to a bug (hah!), so I changed it. If you ever encounter a real bug, please tell me immediately!
# Permissive parser parser = PDBParser(PERMISSIVE=1) parser = PDBParser() # The same (default) # Strict parser strict_parser = PDBParser(PERMISSIVE=0)
In the permissive state (DEFAULT), PDB files that obviously contain errors are 'corrected' (i.e. some residues or atoms are left out). These errors include:
- Multiple residues with the same identifier
- Multiple atoms with the same identifier (taking into account the altloc identifier)
These errors indicate real problems in the PDB file (for details see the Bioinformatics article). In the restrictive state, PDB files with errors cause an exception to occur. This is useful to find errors in PDB files.
Some errors however are automatically corrected. Normally each disordered atom should have a non-blank altloc identifier. However, there are many structures that do not follow this convention, and have a blank and a non-blank identifier for two disordered positions of the same atom. This is automatically interpreted in the right way.
Sometimes a structure contains a list of residues belonging to chain A, followed by residues belonging to chain B, and again followed by residues belonging to chain A, i.e. the chains are 'broken'. This is also correctly interpreted.
Can I write PDB files?
Use the PDBIO class for this. It's easy to write out specific parts of a structure too, of course.
Example: saving a structure
io = PDBIO() io.set_structure(s) io.save('out.pdb')
If you want to write out a part of the structure, make use of the
class (also in PDBIO
). Select has four methods:
accept_model(model) accept_chain(chain) accept_residue(residue) accept_atom(atom)
By default, every method returns 1 (which means the model/chain/residue/atom
is included in the output). By subclassing Select
and returning
0 when appropriate you can exclude models, chains, etc. from the output.
Cumbersome maybe, but very powerful. The following code only writes
out glycine residues:
class GlySelect(Select): def accept_residue(self, residue): if residue.get_name()=='GLY': return 1 else: return 0 io = PDBIO() io.set_structure(s) io.save('gly_only.pdb', GlySelect())
If this is all too complicated for you, the Dice
module contains
a handy extract
function that writes out all residues in
a chain between a start and end residue.
Can I write mmCIF files?
No, and I also don't have plans to add that functionality soon (or ever - I don't need it at all, and it's a lot of work, plus no-one has ever asked for it). People who want to add this can contact me.
The Structure object
What's the overall layout of a Structure object?
The Structure
object follows the so-called SMCRA
(Structure/Model/Chain/Residue/Atom) architecture :
\item A structure consists of models
\item A model consists of chains
\item A chain consists of residues
\item A residue consists of atoms
This is the way many structural biologists/bioinformaticians think
about structure, and provides a simple but efficient way to deal with
structure. Additional stuff is essentially added when needed. A UML
diagram of the Structure
object (forget about the Disordered
classes for now) is shown in Fig. \ref{cap:SMCRA.
% \begin{figure[tbh] \begin{center\includegraphics[%
width=100mm, keepaspectratio]{images/smcra.png\end{center
\caption{\label{cap:SMCRAUML diagram of SMCRA architecture of the Structure
object. Full lines with diamonds denote aggregation, full lines with
arrows denote referencing, full lines with triangles denote inheritance
and dashed lines with triangles denote interface realization.
The following code iterates through all atoms of a structure:
p = PDBParser() structure = p.get_structure('X', 'pdb1fat.ent') for model in structure: for chain in model: for residue in chain: for atom in residue: print atom
There are also some shortcuts:
# Iterate over all atoms in a structure for atom in structure.get_atoms(): print atom # Iterate over all residues in a model for residue in model.get_residues(): print residue
Structures, models, chains, residues and atoms are called Entities
in Biopython. You can always get a parent Entity
from a child
, e.g.:
residue = atom.get_parent() chain = residue.get_parent()
You can also test whether an Entity
has a certain child using
the has_id
Can I do that a bit more conveniently?
You can do things like:
atoms = structure.get_atoms() residues = structure.get_residues() atoms = chain.get_atoms()
You can also use the Selection.unfold_entities
# Get all residues from a structure res_list = Selection.unfold_entities(structure, 'R') # Get all atoms from a chain atom_list = Selection.unfold_entities(chain, 'A')
Obviously, A
=atom, R
=residue, C
=chain, M
=model, S
You can use this to go up in the hierarchy, e.g. to get a list of (unique) Residue
or Chain
parents from a list of
residue_list = Selection.unfold_entities(atom_list, 'R') chain_list = Selection.unfold_entities(atom_list, 'C')
For more info, see the API documentation.
How do I extract a specific Atom
from a Structure
Easy. Here are some examples:
model = structure[0] chain = model['A'] residue = chain[100] atom = residue['CA']
Note that you can use a shortcut:
atom = structure[0]['A'][100]['CA']
What is a model id?
The model id is an integer which denotes the rank of the model in the PDB/mmCIF file. The model is starts at 0. Crystal structures generally have only one model (with id 0), while NMR files usually have several models.
What is a chain id?
The chain id is specified in the PDB/mmCIF file, and is a single character (typically a letter).
What is a residue id?
This is a bit more complicated, due to the clumsy PDB format. A residue id is a tuple with three elements:
- The hetero-flag: this is
plus the name of the hetero-residue (e.g.'H_GLC'
in the case of a glucose molecule), or'W'
in the case of a water molecule. - The sequence identifier in the chain, e.g. 100
- The insertion code, e.g.
. The insertion code is sometimes used to preserve a certain desirable residue numbering scheme. A Ser 80 insertion mutant (inserted e.g. between a Thr 80 and an Asn 81 residue) could e.g. have sequence identifiers and insertion codes as follows: Thr 80 A, Ser 80 B, Asn 81. In this way the residue numbering scheme stays in tune with that of the wild type structure.
The id of the above glucose residue would thus be ('H_GLC', 100, 'A')
. If the hetero-flag and insertion code are blank, the sequence
identifier alone can be used:
# Full id residue = chain[(' ', 100, ' ')] # Shortcut id residue = chain[100]
The reason for the hetero-flag is that many, many PDB files use the same sequence identifier for an amino acid and a hetero-residue or a water, which would create obvious problems if the hetero-flag was not used.
What is an atom id?
The atom id is simply the atom name (eg. 'CA'
). In practice,
the atom name is created by stripping all spaces from the atom name
in the PDB file.
However, in PDB files, a space can be part of an atom name. Often,
calcium atoms are called 'CA..'
in order to distinguish them
from Cα atoms (which are called '.CA.'
). In cases
were stripping the spaces would create problems (ie. two atoms called
in the same residue) the spaces are kept.
How is disorder handled?
This is one of the strong points of Bio.PDB. It can handle both disordered atoms and point mutations (ie. a Gly and an Ala residue in the same position).
Disorder should be dealt with from two points of view: the atom and the residue points of view. In general, I have tried to encapsulate all the complexity that arises from disorder. If you just want to loop over all Cα atoms, you do not care that some residues have a disordered side chain. On the other hand it should also be possible to represent disorder completely in the data structure. Therefore, disordered atoms or residues are stored in special objects that behave as if there is no disorder. This is done by only representing a subset of the disordered atoms or residues. Which subset is picked (e.g. which of the two disordered OG side chain atom positions of a Ser residue is used) can be specified by the user.
Disordered atom positions are represented by ordinary Atom
objects, but all Atom
objects that represent the same physical
atom are stored in a DisorderedAtom
object (see Fig. \ref{cap:SMCRA).
Each Atom
object in a DisorderedAtom
object can
be uniquely indexed using its altloc specifier. The DisorderedAtom
object forwards all uncaught method calls to the selected Atom object,
by default the one that represents the atom with the highest
occupancy. The user can of course change the selected Atom
object, making use of its altloc specifier. In this way atom disorder
is represented correctly without much additional complexity. In other
words, if you are not interested in atom disorder, you will not be
bothered by it.
Each disordered atom has a characteristic altloc identifier. You can
specify that a DisorderedAtom
object should behave like
the Atom
object associated with a specific altloc identifier:
atom.disordered_select('A') # select altloc A atom atom.disordered_select('B') # select altloc B atom
A special case arises when disorder is due to point mutations, i.e. when two or more point mutants of a polypeptide are present in the crystal. An example of this can be found in PDB structure 1EN2.
Since these residues belong to a different residue type (e.g. let's
say Ser 60 and Cys 60) they should not be stored in a single Residue
object as in the common case. In this case, each residue is represented
by one Residue
object, and both Residue
are stored in a single DisorderedResidue
object (see Fig.
The DisorderedResidue
object forwards all uncaught
methods to the selected Residue
object (by default the last
object added), and thus behaves like an ordinary
residue. Each Residue
object in a DisorderedResidue
object can be uniquely identified by its residue name. In the above
example, residue Ser 60 would have id 'SER' in the DisorderedResidue
object, while residue Cys 60 would have id 'CYS'. The user can select
the active Residue
object in a DisorderedResidue
object via this id.
Example: suppose that a chain has a point mutation at position 10, consisting of a Ser and a Cys residue. Make sure that residue 10 of this chain behaves as the Cys residue.
residue = chain[10] residue.disordered_select('CYS')
In addition, you can get a list of all Atom
objects (ie.
all DisorderedAtom
objects are 'unpacked' to their individual
objects) using the get_unpacked_list
of a (Disordered
Can I sort residues in a chain somehow?
Yes, kinda, but I'm waiting for a request for this feature to finish it :-).
How are ligands and solvent handled?
See 'What is a residue id?'.
What about B factors?
Well, yes! Bio.PDB supports isotropic and anisotropic B factors, and also deals with standard deviations of anisotropic B factor if present (see the section #Analysis).
What about standard deviation of atomic positions?
Yup, supported. See the section #Analysis.
I think the SMCRA data structure is not flexible/sexy/whatever enough...
Sure, sure. Everybody is always coming up with (mostly vaporware or partly implemented) data structures that handle all possible situations and are extensible in all thinkable (and unthinkable) ways. The prosaic truth however is that 99.9\% of people using (and I mean really using!) crystal structures think in terms of models, chains, residues and atoms. The philosophy of Bio.PDB is to provide a reasonably fast, clean, simple, but complete data structure to access structure data. The proof of the pudding is in the eating.
Moreover, it is quite easy to build more specialised data structures
on top of the Structure
class (eg. there's a Polypeptide
class). On the other hand, the Structure
object is built
using a Parser/Consumer approach (called PDBParser
and StructureBuilder
, respectively). One can easily reuse
the PDB/mmCIF parsers by implementing a specialised StructureBuilder
class. It is of course also trivial to add support for new file formats
by writing new parsers.
How do I extract information from an Atom
Using the following methods:
a.get_name() # atom name (spaces stripped, e.g. 'CA') a.get_id() # id (equals atom name) a.get_coord() # atomic coordinates a.get_vector() # atomic coordinates as Vector object a.get_bfactor() # isotropic B factor a.get_occupancy() # occupancy a.get_altloc() # alternative location specifier a.get_sigatm() # std. dev. of atomic parameters a.get_siguij() # std. dev. of anisotropic B factor a.get_anisou() # anisotropic B factor a.get_fullname() # atom name (with spaces, e.g. '.CA.')
How do I extract information from a Residue
Using the following methods:
r.get_resname() # return the residue name (eg. 'GLY') r.is_disordered() # 1 if the residue has disordered atoms r.get_segid() # return the SEGID r.has_id(name) # test if a residue has a certain atom
How do I measure distances?
That's simple: the minus operator for atoms has been overloaded to return the distance between two atoms.
# Get some atoms ca1 = residue1['CA'] ca2 = residue2['CA'] # Simply subtract the atoms to get their distance distance = ca1-ca2
How do I measure angles?
This can easily be done via the vector representation of the atomic
coordinates, and the calc_angle
function from the Vector
vector1=atom1.get_vector() vector2=atom2.get_vector() vector3=atom3.get_vector() angle=calc_angle(vector1, vector2, vector3)
How do I measure torsion angles?
Again, this can easily be done via the vector representation of the
atomic coordinates, this time using the calc_dihedral
from the Vector
vector1=atom1.get_vector() vector2=atom2.get_vector() vector3=atom3.get_vector() vector4=atom4.get_vector() angle=calc_dihedral(vector1, vector2, vector3, vector4)
How do I determine atom-atom contacts?
Use NeighborSearch
. This uses a KD tree data structure coded
in C behind the screens, so it's pretty darn fast (see Bio.KDTree
How do I extract polypeptides from a Structure
Use PolypeptideBuilder
. You can use the resulting Polypeptide
object to get the sequence as a Seq
object or to get a list
of Cα atoms as well. Polypeptides can be built using a C-N
or a Cα-Cα distance criterion.
# Using C-N ppb=PPBuilder() for pp in ppb.build_peptides(structure): print pp.get_sequence() # Using CA-CA ppb=CaPPBuilder() for pp in ppb.build_peptides(structure): print pp.get_sequence()
Note that in the above case only model 0 of the structure is considered
by PolypeptideBuilder
. However, it is possible to use PolypeptideBuilder
to build Polypeptide
objects from Model
and Chain
objects as well.
How do I get the sequence of a structure?
The first thing to do is to extract all polypeptides from the structure
(see previous entry). The sequence of each polypeptide can then easily
be obtained from the Polypeptide
objects. The sequence is
represented as a Biopython Seq
object, and its alphabet is
defined by a ProteinAlphabet
>\,{>\,{> seq=polypeptide.get_sequence() >\,{>\,{> print seq Seq('SNVVE...', <class Bio.Alphabet.ProteinAlphabet>)
How do I determine secondary structure?
For this functionality, you need to install DSSP (and obtain a license
for it - free for academic use, see http://www.cmbi.kun.nl/gv/dssp/).
Then use the DSSP
class, which maps Residue
to their secondary structure (and accessible surface area). The DSSP
codes are listed in Table \ref{cap:DSSP-codes. Note that DSSP (the
program, and thus by consequence the class) cannot handle multiple
% \begin{table
==== \begin{tabular{|c|c| \hline Code& Secondary structure\tabularnewline \hline \hline H& α-helix\tabularnewline \hline B& Isolated β-bridge residue\tabularnewline \hline E& Strand \tabularnewline \hline G& 3-10 helix \tabularnewline \hline I& $\Pi$-helix \tabularnewline \hline T& Turn\tabularnewline \hline S& Bend \tabularnewline \hline -& Other\tabularnewline \hline \end{tabular
\caption{\label{cap:DSSP-codesDSSP codes in Bio.PDB.
How do I calculate the accessible surface area of a residue?
Use the DSSP
class (see also previous entry). But see also
next entry.
How do I calculate residue depth?
Residue depth is the average distance of a residue's atoms from the
solvent accessible surface. It's a fairly new and very powerful parameterization
of solvent accessibility. For this functionality, you need to install
Michel Sanner's MSMS program (http://www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html).
Then use the ResidueDepth
class. This class behaves as a
dictionary which maps Residue
objects to corresponding (residue
depth, Cα depth) tuples. The Cα depth is the distance
of a residue's Cα atom to the solvent accessible surface.
model = structure[0] rd = ResidueDepth(model, pdb_file) residue_depth, ca_depth=rd[some_residue]
You can also get access to the molecular surface itself (via the get_surface
function), in the form of a Numeric python array with the surface points.
How do I calculate Half Sphere Exposure?
Half Sphere Exposure (HSE) is a new, 2D measure of solvent exposure. Basically, it counts the number of Cα atoms around a residue in the direction of its side chain, and in the opposite direction (within a radius of 13 Å). Despite its simplicity, it outperforms many other measures of solvent exposure. An article describing this novel 2D measure has been submitted.
HSE comes in two flavors: HSEα and HSEβ. The former
only uses the Cα atom positions, while the latter uses the
Cα and Cβ atom positions. The HSE measure is calculated
by the HSExposure
class, which can also calculate the contact
number. The latter class has methods which return dictionaries that
map a Residue
object to its corresponding HSEα, HSEβ
and contact number values.
model = structure[0] hse = HSExposure() # Calculate HSEalpha exp_ca=hse.calc_hs_exposure(model, option='CA3') # Calculate HSEbeta exp_cb=hse.calc_hs_exposure(model, option='CB') # Calculate classical coordination number exp_fs=hse.calc_fs_exposure(model) # Print HSEalpha for a residue print exp_ca[some_residue]
First, create an alignment file in FASTA format, then use the StructureAlignment
class. This class can also be used for alignments with more than two
How do I test if a Residue object is an amino acid?
Use is_aa(residue)
Can I do vector operations on atomic coordinates?
objects return a Vector
object representation
of the coordinates with the get_vector
method. Vector
implements the full set of 3D vector operations, matrix multiplication
(left and right) and some advanced rotation-related operations as
well. See also next question.
How do I put a virtual Cβ on a Gly residue?
OK, I admit, this example is only present to show off the possibilities
of Bio.PDB's Vector
module (though this code is actually
used in the HSExposure
module, which contains a novel way
to parametrize residue exposure - publication underway). Suppose that
you would like to find the position of a Gly residue's Cβ atom,
if it had one. How would you do that? Well, rotating the N atom of
the Gly residue along the Cα-C bond over -120 degrees roughly
puts it in the position of a virtual Cβ atom. Here's how to
do it, making use of the rotaxis
method (which can be used
to construct a rotation around a certain axis) of the Vector
# get atom coordinates as vectors n = residue['N'].get_vector() c = residue['C'].get_vector() ca = residue['CA'].get_vector() # center at origin n = n - ca c = c - ca # find rotation matrix that rotates n -120 degrees along the ca-c vector rot = rotaxis(-pi{*120.0/180.0, c) # apply rotation to ca-n vector cb_at_origin = n.left_multiply(rot) # put on top of ca atom cb = cb_at_origin + ca
This example shows that it's possible to do some quite nontrivial
vector operations on atomic data, which can be quite useful. In addition
to all the usual vector operations (cross (use **
), and
dot (use *
) product, angle, norm, etc.) and the above mentioned
rotaxis function, the <code>Vector module also has methods
to rotate (<code>rotmat
) or reflect (refmat
) one vector
on top of another.
Manipulating the structure
How do I superimpose two structures?
Surprisingly, this is done using the Superimposer
This object calculates the rotation and translation matrix that rotates
two lists of atoms on top of each other in such a way that their RMSD
is minimized. Of course, the two lists need to contain the same amount
of atoms. The Superimposer
object can also apply the rotation/translation
to a list of atoms. The rotation and translation are stored as a tuple
in the rotran
attribute of the Superimposer
(note that the rotation is right multiplying!). The RMSD is stored
in the rmsd
The algorithm used by Superimposer
comes from \textit{Matrix
computations, 2nd ed. Golub, G. \& Van Loan (1989) and makes use
of singular value decomposition (this is implemented in the general
sup=Superimposer() # Specify the atom lists # 'fixed' and 'moving' are lists of Atom objects # The moving atoms will be put on the fixed atoms sup.set_atoms(fixed, moving) # Print rotation/translation/rmsd print sup.rotran print sup.rms # Apply rotation/translation to the moving atoms sup.apply(moving)
How do I superimpose two structures based on their active sites?
Pretty easily. Use the active site atoms to calculate the rotation/translation matrices (see above), and apply these to the whole molecule.
Can I manipulate the atomic coordinates?
Yes, using the transform
method of the Atom
or directly using the set_coord
Other Structural Bioinformatics modules
See the main Biopython tutorial.
No documentation available yet.
You haven't answered my question yet!
Woah! It's late and I'm tired, and a glass of excellent Pedro Ximenez sherry is waiting for me. Just drop me a mail, and I'll answer you in the morning (with a bit of luck...).
The main author/maintainer of Bio.PDB is:
Thomas Hamelryck Bioinformatics center Institute of Molecular Biology University of Copenhagen Universitetsparken 15, Bygning 10 DK-2100 København Ø Denmark email@example.com
Kristian Rother donated code to interact with the PDB database, and to parse the PDB
header. Indraneel Majumdar sent in some bug reports and assisted in
coding the Polypeptide
module. Many thanks to Brad Chapman,
Jeffrey Chang, Andrew Dalke and Iddo Friedberg for suggestions, comments,
help and/or biting criticism :-).
Can I contribute?
Yes, yes, yes! Just send me an e-mail (email@example.com) or to the Biopython developers (email@example.com) if you have something useful to contribute! Eternal fame awaits!


text:
Check out some available loans that are similar to this one!
Shirly requested this loan to purchase fertilizers and other farm inputs.She hopes to have a successful business in the future.
Additional Information
More information about this loan
On Friday November 8, 2013, Super Typhoon Haiyan made its way through Southeast Asia, causing substantial damage to homes and businesses in areas of the Philippines. Given the state of devastation following this storm, borrowers living and working in these areas may have difficulty making repayments on their loans, thus making their Kiva loans higher risk. More information >>
About Community Economic Ventures, Inc.
Community Economic Ventures, Inc. (CEVI), based in Bohol, was awarded the Platinum Award for Transparency in Social Performance Reporting by CGAP. Social performance monitoring is imperative in measuring a microfinance institution's effectiveness. The fact that CEVI is participating in this process speaks volumes about the organization's commitment to serving its clients effectively. In addition to providing credit for its clients, CEVI provides savings, insurance, and training through regular cluster group meetings.You can show your support for CEVI by joining the Friends of CEVI Kiva Lending Team. Learn more by visiting the CEVI website.
About Philippines
979View loans »
Success!! The loan was 100% repaid
A loan of $375 helped Shirly to purchase fertilizers and other farm inputs.
- Repayment Term
- 7 months (Additional Information)
- Repayment Schedule
- At end of term
- Pre-Disbursed:
- Sep 13, 2011
- Listed
- Sep 23, 2011
- Currency Exchange Loss:
- Covered
- Ended:
- Mar 15, 2012

subset: commoncrawl


text:
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Showing items 141 - 160 of 533
Showing items 141 - 160 of 533


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Any commercial use of information within this site or linked to by this site is prohibited without prior permission. You may though use the information for personal or academic purposes. Map data is copyright by the respective copyright holders. House Price information including property price trends are based on analysis by PROVISER of UK actual house sold price information and is copyright PROVISER. Whilst every effort has been made to try to ensure the accuracy of information on this site, We cannot guarantee that it is all accurate or up-to-date. You should ensure that you confirm any information that you will rely on with the appropriate source.


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The original deal pioneer keeps on pinching pennies and cracking wise. No, that price isn't a typo.
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"I'm a refrigerator whore!" "I'm hungry, but I ate all my nuts. I have to eat my chocolate balls instead."
Really, I'm more respectable than I look
Volunteer Moderator
just bored and bumping threads
"Why didn't you get me anything?" "It's Administrative Assistants' Day, not Administrative Assistants' Assistants' Day."
"Science is a set of values imposed on us by the liberals"
"She said she was having office hours in the afternoon. It's now 12:30, where is she?" Looks on sign up sheet "What?!? She doesn't have office hours until 4 PM. Happy hour starts at 4!"
"Yes, I know, but you have to let go of the fear. You have to let go!"
Mavyn wrote:"Yes, I know, but you have to let go of the fear. You have to let go!"
The only thing you have to fear is fear itself?
Home office, so might not count. SO on the phone with his (English) mom. "We made a bunch of bangers over the weekend, so that's dinner tonight."
[quote postid="4483513" user="Mavyn"]Home office, so might not count. SO on the phone with his (English) mom.
"I get my adrenalines going"
dontwantaname wrote:just bored and bumping threads
1. i didn't know you worked in an office! 2. i wish i worked in an office where bumping threads could be openly discussed like that.
Read at the office: Please remove the red attribute from all text. Although it was in the prototype, it wasn't meant to be in the actual report.
I think they have a rule that you need to have pants on if you are working with the kids
Female co-worker: if you've never fallen in your @ss must be HUGE. Male co-worker: no, my eyes work perfectly.
This tip is too wide, and this tip is too small.
kenney9226 wrote:This tip is too wide, and this tip is too small.
"But this tip is JUUUUUST right!" Sounds like something out of a prOn version of Goldilocks and the Three Bears. Or, Goldilicks and the Three Bares.
"It's different with you. You never walk anywhere...you don't even go to the mall because of the walking."
Mavyn wrote:"It's different with you. You never walk anywhere...you don't even go to the mall because of the walking."
I know a lot of people that don't go to malls because of all the walking. Most of them have bad backs and just can't do it.
lplady wrote:I know a lot of people that don't go to malls because of all the walking. Most of them have bad backs and just can't do it.
The irony there is that being more active would likely help their backs far more than getting less exercise. On the campus I work on, walking is easy. There are lots of paths, and it's a mile walk round trip just getting to and from the parking lot. They have shuttles, but it's actually slower to take the shuttle, since I'd be the last stop on the loop.
"Fashion plate?!?! She's the whole buffet table!!"
"It's pretty long... but it's not that hard."
"He's going to keep licking it!"
"Well, I'm peeing right now, but also trying to hold in a fart at the same time. So I can't really talk..."
"You're the only one I know who can take a hsit around corners. How do you even get that crap there?"
"My balls light up too"
"If you want me to feel your butt, I will."
two female coworkers to me (a man): "Kenny, do you want to go to the restroom with us?" I foolishly declined.
Hey, these bongos make a great laptop stand.
From Boss to file clerk: "Sharon*, will you make me a salad?" *Name changed to protect the innocent.
"Will you stop coming into my office and taking your clothes off?"
"Oh. So that's why the birds are angry?"
"My buns keep getting bigger!"
"There is certainly uncertainty."
"Kenny just 'juggled my apples!'"
kenney9226 wrote:"Kenny just 'juggled my apples!'"
I'm guessing if I worked with you, that wouldn't be that odd. (unless it is some sort of sex thing)
"best thing about that show is that it has nothing to do with donkeys or midgets"
In a restaurant: "Hi, I haven't seen you in a long time." "I haven't seen you in a long time either." ???
pooflady wrote:In a restaurant: "Hi, I haven't seen you in a long time." "I haven't seen you in a long time either." ???
i.e. not a stalker.
j5 wrote:i.e. not a stalker.
i.e. I recognize you so I'm going to say hi, but I'll be damned if I know your name. Oh Potty Emergency!, you said hi to me with familiarity, um hi back mystery person I knew once.


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Daily Archives: Thursday, April 17, 2014
If you can help reader John please leave a message in the blog. John, Do you have any leads on a part time personal chef? My wife and I have vastly different diets (I am vegan and she is Paleo) … Continue reading
The sun is shining and the days are longer which means this is patio season. Just in time for guests to enjoy the great outdoors, Arlington Tavern at 21 W. Victoria Street has opened their new front patio (on the … Continue reading
The nonprofit Santa Barbara Culinary Arts (SBCA) has announced a fund-raising cookbook launch party on Saturday, May 3rd from 1-3 p.m. at the Gourmet Dining Room, School of Culinary Arts & Hotel Management at Santa Barbara City College. Taste the … Continue reading


text:
The original deal pioneer keeps on pinching pennies and cracking wise. No, that price isn't a typo.
Go to Woot
Candlepower and puppet shows are so passé. Get the newest TVs, speakers, home theater gear, and more.
Go to Electronics.Woot
The robots are coming! And so are the laptops, the tablets, the chargers, and all sorts of other gadgets!
Go to Computers.Woot
High living at low prices with name-brand deals for your pad, crib, nest, or castle - inside and out.
Go to Home.Woot
Make it, build it, improve it. But whatever home project you've got in mind, start by saving money on it.
Go to Tools & Garden
Sports, fitness, and outdoors deals, because saving money is only one of your passions.
Go to Sport.Woot
You don't have to spend a lot to look like you do. Werk it and twerk it with amazing deals on designer watches, handbags and more.
Go to Accessories & Watches
Deals for moms and dads and anybody else who needs kids' stuff, from toys to baby gear to furniture to clothing.
Go to Kids.Woot
Our exclusive graphic tees will make you laugh, will make you cry, will make you look totally hot.
Go to Shirt.Woot
Direct from the winery to your thirsty lips: wine deals worth doing a spit-take over.
Go to Wine.Woot
Last chance deals for hardcore cheapskates. Catch 'em before they - you guessed it - sell out.
Go to Sellout.Woot
460,636 deals (and counting) from around the web, shared and ranked by a community of deal fiends like you. Go to Deals.Woot.
Volunteer Moderator
stacipurv wrote:pattern maker
make love
dontwantaname wrote:make love
love seat
GodfatherND wrote:love seat
seat cushion
stacipurv wrote:seat cushion
cushion cut
pooflady wrote:cushion cut
cut rate
dontwantaname wrote:cut rate
rate hike
pooflady wrote:rate hike
hiking trail
dontwantaname wrote:hiking trail
trail mix
pooflady wrote:trail mix
mix tape
olcubmaster wrote:mix tape
tape worm
pooflady wrote:tape worm
worm hole
dontwantaname wrote:worm hole
hole card
pooflady wrote:hole card
card shark
dontwantaname wrote:card shark
shark cage
pooflady wrote:shark cage
caged lion
dontwantaname wrote:caged lion
lion's share
pooflady wrote:lion's share
share toys
dontwantaname wrote:share toys
toy store
pooflady wrote:toy store
store clerk
GodfatherND wrote:store clerk
clerk's office
pooflady wrote:clerk's office
office chair
dontwantaname wrote:office chair
chair rail
pooflady wrote:chair rail
rail car
dontwantaname wrote:rail car
car exhaust
pooflady wrote:car exhaust
exhaust pipe
GodfatherND wrote:exhaust pipe
pipe wrench
dontwantaname wrote:pipe wrench
wrench set
olcubmaster wrote:wrench set
set square
GodfatherND wrote:set square
square deal
olcubmaster wrote:square deal
Deal breaker
baybiz wrote:Deal breaker
break even
stacipurv wrote:break even
even keel
olcubmaster wrote:even keel
keel boat
kdeuce wrote:keel boat
boat dock
GodfatherND wrote:boat dock
docking station
stacipurv wrote:docking station
station break
olcubmaster wrote:station break
break wind
pooflady wrote:break wind
wind (I can see that you posted here and not on pwa) storm
dontwantaname wrote:wind (I can see that you posted here and not on pwa) storm
storm chaser
GodfatherND wrote:storm chaser
chase down


text:
Email UKClimbing.com User
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Write simpler, smarter CSS for your WordPress themes and plugins with Sass and Grunt.js.
Build a website to showcase your photography the DIY (do-it-yourself) way, with WordPress and a selection of helpful plugins.
Build a website the DIY (do-it-yourself) way with WordPress and Genesis. This course is the first step, showing how to install, connect, and configure WordPress on your own domain.
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Learn how to edit WordPress user accounts directly in the database with phpMyAdmin—bypassing WordPress entirely.
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Learn how to build a WordPress theme from scratch using the _s (aka Underscores) starter theme.
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Explore how to integrate WordPress into a Dreamweaver site to make for efficient editing of your code.
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Learn how to create your own website or blog with WordPress.com—the free, easy-to-use service that is democratizing publishing on the web.
Drive more visitors to your WordPress site by performing search engine optimization, or SEO, with the help of two powerful plugins.
Set up a video blog using WordPress and three different free themes—Twenty Twelve, Origami, and Sundance—and get three completely different looks for your site.
Takes you through the process of making a Drupal website that automatically tailors and sizes content for a wide range of displays, from desktops to mobile devices.
Set up an online magazine using WordPress and three different themes that result in three completely different looks—Max Magazine, Path, and Oxygen.
Extend your Drupal 7 sites with custom modules, which allow you to create everything from admin interfaces to forms.
Demonstrates different design strategies, best practices, and actual code examples for creating a web site that can adapt to multiple devices, screen sizes, and browsers.
Create a network of sites and blogs from a single installation of WordPress with the WordPress Multisite feature.
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more from our members »


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Renée Elise Goldsberry and Fred Weller star in Encores! presentation of the groundbreaking '70s feminist folk musical I'm Getting My Act Together and Taking It on the Road, about a divorced pop star looking to make a big change.
A slew of stars were part of Fun Home's opening night welcome wagon on April 19 at Circle in the Square Theatre! Get a front-row seat to the festivities and the post-show party at Urbo.
April 20, 2015Fun Home features three performers (Beth Malone, Emily Skeggs & Sydney Lucas) playing the central character in this poignant musical memoir.
April 20, 2015Laura Michelle Kelly has her camera hijacked by Matthew Morrison in a very special behind-the-scenes video at Finding Neverland.
April 18, 2015A sneak peek of Amra Faye-Wright and Chicago's new Roxie, Brandy Norwood, doing the "Hot Honey Rag."
April 17, 2015A sneak peek of Amra Faye-Wright and Chicago's new Roxie, Brandy Norwood, and singing "Nowadays."
April 17, 2015A sneak peek of Chicago's new Roxie, Brandy Norwood, singing "Roxie."
April 17, 2015Doctor Zhivago's Tam Mutu and Kelli Barrett on their diner obsessions, fantasy band names and what kind of wine to serve Javert and the Phantom.
April 17, 2015The name on everybody's lips is Brandy Norwood! Broadway.com catches up with the Grammy winner in rehearsal as she prepares to step into Roxie's heels in Chicago.
April 17, 2015Two-time Tony Award winner Sutton Foster makes her fourth appearance on Show People, talking up her hilarious TV Land show Younger.
April 16, 2015Go behind the lens with Caitlin McNaney as she shoots the Something Rotten clowns Brooks Ashmanskas, Peter Bartlett, Gerry Vichi and Brad Oscar.
April 16, 2015Believe! Broadway.com talks to Matthew Morrison, Laura Michelle Kelly and all the stars at the opening night of Finding Neverland.
April 16, 2015Check out Matthew Morrison, Kelsey Grammer, Laura Michelle Kelly and the cast of Finding Neverland sing songs including "Believe," "Stronger" and "All That Matters."
April 16, 2015


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Illinois Fighting Illini Gear
(1460 items)
Product ID: 653379
Main Content
Proudly represent the Fighting Illini's victorious and storied past when you decorate your office or fan cave with this full-size Throwback Suspension helmet from Riddell! From the retro-style team graphics and vibrant striping right down to the vintage two-bar face mask and authentic web suspension construction, it's designed to resemble the original helmets worn by the 1964 Illinois football team, making it the perfect lasting addition to any fan's collection!
- 2-Point chin strap
- Great for autographs
- Made in the USA
- Not meant for active/recreational use
- Official team designs and decals
- Officially licensed collegiate product
- Polycarbonate full-size throwback helmet
- Vintage two-bar facemask
- Web suspension system in a rounded shell
Illini Customers also liked:
Special event items are produced by manufacturers only after the outcome of a game
or event. These are advanced sale items and will ship immediately after they are
received in our warehouse.
Manufacturer direct items are shipped directly from the manufacturer. These items
are not available for international or expedited shipping.
Customized items can be personalized with options such as your name, your favorite
number, and/or designs. Some options may be limited by league rules.


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Posted on Wednesday, November 17th, 2010 by Peter Sciretta
More Images in this Gallery:
Comment Now!
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Oscar Isaac 'Ex Machina' Interview: How Stanley Kubrick Influenced His Character, Plus Star Wars and X-Men
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Everything You Need to Remember From 'Game of Thrones' Season 4


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:: Stringing-along 419 scammers for my amusement :: |
This is just one type of the thousands of scam e-mail variants sent out each day by 419 scammers. If you've received an e-mail even remotely similar to the scam published here or if you have arrived at this page via an internet search resulting from an e-mail that you received, YOU HAVE RECEIVED A SCAM E-MAIL! DR. KEVIN KWESI
This is just a small sampling of the many hundreds of advance fee fraud e-mails received each day here at 419BAITER headquarters. It is 100% pure B.S. Purity Guaranteed! There are many different types of 419 scam (examples) but they all promise you something (fortune, job with salary / commision, low-interest loan, lottery prize, bargain gold dust / diamonds, work visa, etc.) in return for a small 'fee' or some kind of remittance. Of course, there is no fortune, no job, no loan, no prize to be had. It's just a ploy to get you to willingly send them money. If you receive one of these scam mails, simply delete it as you would any other spam mails. To see what this site is really all about, visit The Games section. The list of FRESH scammers' e-mail addresses Fresh scam e-mails index #1 | Fresh scam e-mails index #2 | Fresh scam e-mails index #3 Home | Games | Failed Games | Testimonials | About 419 Scams | Scam E-mail Examples Scambaiting Tips and Resources | Links | Contact Information | Privacy Policy |


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Main Content
After celebrating a big Buckeyes win, you finally head to bed, knowing that you need all the sleep you can get before the morning comes. Before you hit the pillow, turn on this spirited Ohio State Vintage art glass nightlight so you can doze off in the soft glow of your team pride. This hand-painted nightlight features a Buckeyes logo in the middle of the glass with a team-colored border around the edges. Using this nightlight is the perfect way to show your team spirit and will prevent any stubbed toes if you have to get up in the middle of the night. Now nothing can stop you from dreaming of Buckeyes victories all night long.
- Hand-painted glass
- Imported
- Indoor use only
- Measures approx. 5" x 4"
- Officially licensed collegiate product
- On/Off switch on front
- Team logo and colors
- Uses 5W maximum C7 bulb (included)
Buckeyes Customers also liked:
Special event items are produced by manufacturers only after the outcome of a game
or event. These are advanced sale items and will ship immediately after they are
received in our warehouse.
Manufacturer direct items are shipped directly from the manufacturer. These items
are not available for international or expedited shipping.
Customized items can be personalized with options such as your name, your favorite
number, and/or designs. Some options may be limited by league rules.


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3.13. 151.thiệu Khánh Group
Additional Information
About Thanh Hoa Fund for Poor Women (FPW)
Thanh Hoa Fund for Poor Women (FPW) works to provide credit to women and their families in the central Vietnamese province of Thanh Hoa, one of the poorest regions of the country. The institution's target clients are poor and low-income women who have the ability to work but lack the capital. Accordingly, FPW prioritizes single mothers, low-income women with children who have dropped out of primary school, and Viet Nam's poorest women who cannot access any formal financial services.This is a Group Loan
In a group loan, each member of the group receives an individual loan but is part of a larger group of individuals. The group is there to provide support to the members and to provide a system of peer pressure, but groups may or may not be formally bound by a group guarantee. In cases where there is a group guarantee, members of the group are responsible for paying back the loans of their fellow group members in the case of delinquency or default.
Kiva's Field Partners typically feature one borrower from a group. The loan description, sector, and other attributes for a group loan profile are determined by the featured borrower's loan. The other members of the group are not required to use their loans for the same purpose.
About Vietnam
147View loans »
Success!! The loan was 100% repaid
- Repayment Term
- 14 months (Additional Information)
- Repayment Schedule
- Monthly
- Pre-Disbursed:
- Apr 15, 2012
- Listed
- May 6, 2012
- Currency Exchange Loss:
- Possible
- Ended:
- May 17, 2013


text:
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Home > Home & Office > Kitchen >
"Spork Sweater!"
Spoons for censorship
That's a lotta sporks!
Ramen tastes better with a spork
What noms may come
Do I have something on my face?
Srs spork bsns
Survival kit
How meta
Spork vs. Dinty Moore
Oh, the talent
First stop for new spork - ice cream!
Her enchanted spork - quantum-ly delicious
Good to the last sporkfull
Wedding sporks
Spork the rainbow!
Best not eat that
Is that a bowl of dirt?
Having jettisoned the human crew, it was time to enjoy tasty tre
Sporkin' through Africa
Chunky soup requires a spork
Seriously, this implement exists! (Don't eat with it.)
Guatemalan noms
DAMMIT JIM! I'm a Spork, not a Spoon!
My spork is too big!
Sporkin' some road food
So good, you can eat it out of the jar!
Defending freedom, one spork at a time
1) Eat strawberries. 2) ? 3) Profit!
Rose once killed a man using just this spork
3.14 pies and a spork
See no evil?
Always know where your spork is
Nobody touches Jeff's spork. Nobody.
Save the planet, use titanium!
Don't look a gift spork in the mouth
You never know when you might need it
Everybody was spork-fu fighting
Defying Gravity, Season 1, Episode 8
ThinkGeek adventurer's kit
Spork cordon bleu
Archilon Shadowheart doesn't stand a chance
Plain ol' flowers are boring...
Spork defeats man
conquerer, thy name is moonspork!
Here kitty kitty kitty...
The meal of barbarians.
Titanium tastiness.
Born to be Geeky.
What's actually in that sandwich?
Make your hiccups go away.
Weapon of Mass Destruction
Microwave lunch of champions.
Titanium romance
Everyone's craving Titanium these days.
His tricks will only get better.
Never know when you'll need a spork.
Behold the awesome.
Our favorite kind of geek.
One spork to rule them all.
Cut thru the New Zealand sunset.
Spork in the field.
gotta get spork in time.
this spork is bananas, B-A-N-A-N-A-S
O Lord of Lunch, smile upon this, thy most perfect utensil!
Alien paw
Balancing act
Hail Spork
Was it good for you?
You have a little something stuck to your face
Trusty spork always ready
Merry Sporkmas from The Village People
Near the European Space Agency's Rosetta Satellite Simulator
Batgirl always carries a spork in her utility belt
Timmy will spork out the eyes of his enemies!
Snowbot and the Spork of Doom
Spork on vacation
Spork of Heroes
In the wild.
TGX Tactical BBQ Fork with (flashlight & laser) sight
Tactical Lunch Kit
Collapsible Shot Glass
Eat'N Tool Dark Edition
Das Can-in-Stein
Backpack of Holding


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Puritan En Español
Order by Phone 1-800-645-1030
My Cart: 0 Item(s)|Checkout|Track Order
Lowest Prices, Buy Direct From The Manufacturer, Guaranteed Highest Quality
6 oz Container / Item #037129
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Buy 1 Get 1 Free
2 for $6.99
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text:
Narrow Results
Kirkland's has plenty of pillows to toss around! If you need throw pillows for your couch, or accent pillows for a favorite chair, we have colors and prints to match any room. Our decorative pillows feature printed designs and stitched messages that will fit in with any style.


text:
If you're searching for genealogy records about people named Aamadt who lived in Washington, then you're in just the right place. This directory is designed to help you get complimentary genealogy data about people from your family tree, or anyone else of interest.
Use this section of our directory to see genealogy records from Washington. Look through the list of people who had the last name Aamadt, and click any of them for some complimentary data. The information we display here is taken directly from census and vital records.
Would you like to see information about people with the surname Aamadt from another state? Then stick with this directory. We'll help you look people up by name, state or census decade. Check it out to get free information, and then try a genealogy membership. When you do, you'll have uninterrupted access to comprehensive genealogy reports on anyone in our database. Start today to learn all about your ancestry.


text:
FOR Erica Creer YOU CAN
TCM Messageboards Post your comments here ADD YOUR COMMENT>
Circle Of Iron... Filmed five years after his death, Bruce Lee breaks the mold as co-writer of... more info $14.98was $14.98 Buy Now
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A short but intense police chase went through part of the tarmac at Salt Lake International Airport early Monday morning.
Goblin Valley State Park: A must-see hiking, exploring spot in Utah
Adam Provance, KSL.com Contributor |
posted Apr 27th - 11:32am
Utah has a variety of beautiful mountain ranges and hills that make for a great pastime. If hiking is your thing, check KSL.com each Monday for the "Hike of the Week" to get new ideas of where you can go
Police find 135 grams of meth during Price traffic stop
Geoff Liesik |
posted Apr 27th - 10:21am
Three men were arrested Saturday after Price police say they found 135.9 grams of meth and nearly 16 grams of heroin in a car during a traffic stop.
Spend less, enjoy more: 7 tips for a beautiful yard on a budget
by KSL Local | BrandView
Big visual impact, big savings. These seven tips will help you spend less and enjoy your yard more.
Homeowner chases intruders, fires warning shot
Linda Williams |
posted Apr 27th - 9:59am
A homeowner chased two alleged intruders and fired a warning gunshot Monday morning in Holladay.
Married drivers pay less for car insurance
Bill Gephardt |
posted Apr 27th - 8:20am
Getting married leads to significantly cheaper car insurance premiums.
Salt Lake City bishop named as new Santa Fe archbishop
KSL.com |
posted Apr 27th - 7:56am
The Roman Catholic Church's bishop of Salt Lake City has been appointed the church's new archbishop for Santa Fe, New Mexico.
5 stories you may have missed this weekend
Angela Treasure |
posted Apr 27th - 7:36am
Here are five local stories you may have missed this weekend. As always, click on the headline to read the full story.
Industrial fire closes part of Redwood Road
Shara Park |
posted Apr 27th - 7:35am
Redwood Road reopened after being shut in North Salt Lake between Center Street and I-215 because of an industrial fire.
SLCPD's 'SWAT School' puts potential members through its paces
Mike Debernardo |
posted Apr 26th - 10:55pm
The Salt Lake City Police Department's SWAT training program began this weekend before the sun came up.
Nibley water still not safe to drink
KSL.com |
posted Apr 26th - 10:40pm
Nibley's do not drink order is still in effect Sunday as the city works to make its water supply potable.
Kaysville motorcyclist dies after colliding into semitruck on U.S. 40
Amy Joi O'Donoghue |
posted Apr 26th - 10:39pm
The Utah Highway Patrol reports that Conor Wilson, 23, of Kaysville, died in a Sunday crash while riding his motorcycle. The motorcycle slammed into the back of a slow moving semitrailer hauling a tanker.
Minnesota woman in critical condition after 50-foot fall in Ogden canyon
Ben Dowsett |
posted Apr 26th - 10:27pm
A woman was taken to a hospital via a life flight helicopter after a reported 50-foot fall Sunday in Waterfall Canyon near Ogden, police said.
Utah's Tibetan community prays for those affected by Nepal quake
Amy Joi O'Donoghue |
posted Apr 26th - 10:25pm
Members of Utah's TIbetan community came together Sunday in prayer for those impacted by the devastating earthquake in Nepal. A leader of the Utah Tibetan Association says there are about 30,000 TIbetans in Nepal.
Everyone is invited to the world's largest family reunion
Erin Adair, KSL.com Contributor |
posted Apr 26th - 10:21pm
Thanks to family history technology, people can see how the are related to all 7 billion people on Earth. The world's largest family reunion is set for June 6, and everyone is invited.
U. graduate students' net neutrality-themed video game goes viral
Allison Oligschlaeger |
posted Apr 26th - 8:28pm
The thesis project of 12 University of Utah graduate students, a net neutrality-themed video game, has amassed more than 82,000 downloads and 500 reviews in a week.
Orem father and daughter hiking Everest safe, separated
Sandra Yi |
posted Apr 26th - 7:51pm
A man from Orem and his daughter on Mount Everest are reported to be safe, although they are separated at the moment.
Man allegedly punches officer, arrested after fleeing
Allison Oligschlaeger |
posted Apr 26th - 5:13pm
A West Valley police officer was injured Saturday after a man allegedly punched him in the face and then ran away.
Family reflects on journey of 2 children with physical disabilities
Jen Jacobson |
posted Apr 26th - 4:46pm
After struggling to conceive, Jeff and Brynn Homer realize their challenges don't end after conception. Despite their difficulties, the family keeps an optimistic eye towards the purpose of their children's lives.
Four Utah counties invest $53 million in California port for coal, other exports
Amy Joi O'Donoghue |
posted Apr 26th - 1:09pm
Four counties in Utah secured a $53 million loan from the Community Impact Fund Board to secure access for an Oakland, California, port to ship coal and other commodities. The investment gives the counties nearly half the port's capacity.
Man in custody following hit-and-run, trespassing
Ben Dowsett |
posted Apr 26th - 12:23pm
A man is in custody after fleeing the scene of a hit-and-run Saturday morning, as well as a separate trespassing incident, police said.
Police: German Shepherd breeder disappears with deposits, claims puppies died
Hundreds of Utah children at center of identity theft
High bacteria counts on cellphone doesn't determine rate of infection
By end of high school, nearly all kids have seen pornography, experts say
KSL Investigates: SLC out millions of dollars in unpaid parking tickets
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Jason's DeliDog-Friendly Restaurants25801 H 19 NClearwater,Florida 33763 727-793-0446 Get Map or Directions This health-conscious deli-style restaurant offers a diverse and extensive menu that includes vegetarian/dietary specific choices with a colored coded menu for easy recognition, USDA certified organics, naturally raised meats, and wholesome high quality ingredients. Some offerings include made-from-scratch soups, an organically-inclined fresh salad bar, organic coffee/teas and beverages, specialty sandwiches - or build-your-own, signature dishes, and a kid's menu. Their foods have 0% artificial trans fats, processed MSG, artificial colors, dyes and nitrates, or high fructose corn syrup (a few soda exceptions). Delivery and catering services are offered at most of the delis; they offer community support though a number of venues, and they have implemented programs to reduce their footprint on the environment with more GREEN initiatives planned. Leashed, friendly dogs are allowed at their outside dining area.
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