#LyX 1.3 created this file. For more info see http://www.lyx.org/
\lyxformat 221
\textclass article
\begin_preamble
% header
\usepackage{fancyhdr}
\pagestyle{fancy}
\lhead{Structural Biopython FAQ}
\rhead{}

% remove date
\date{}

% make everything have section numbers
% Make links between references
\usepackage{hyperref}

\newif\ifpdf
\ifx\pdfoutput\undefined
  \pdffalse
\else
  \pdfoutput=1
  \pdftrue
\fi
\ifpdf
  \hypersetup{colorlinks=true, hyperindex=true, citecolor=red, urlcolor=blue}
\fi
\end_preamble
\language english
\inputencoding auto
\fontscheme bookman
\graphics default
\paperfontsize default
\spacing single 
\papersize a4paper
\paperpackage a4
\use_geometry 1
\use_amsmath 0
\use_natbib 0
\use_numerical_citations 0
\paperorientation portrait
\topmargin 20mm
\bottommargin 20mm
\secnumdepth 3
\tocdepth 3
\paragraph_separation indent
\defskip medskip
\quotes_language english
\quotes_times 1
\papercolumns 1
\papersides 1
\paperpagestyle default

\layout Title


\size huge 
The Biopython
\newline 
Structural Bioinformatics FAQ
\layout Author

Thomas Hamelryck
\layout Author


\size normal 
Bioinformatics center
\newline 
Institute of Molecular Biology
\newline 
University of Copenhagen 
\newline 
Universitetsparken 15, Bygning 10
\newline 
DK-2100 Kbenhavn 
\newline 
Denmark 
\newline 
thamelry@binf.ku.dk
\size default 

\newline 

\begin_inset LatexCommand \url{http://www.binf.ku.dk/users/thamelry/}

\end_inset 


\layout Section

Introduction
\layout Standard

The Biopython Project is an international association of developers of freely
 available Python (
\begin_inset LatexCommand \url{http://www.python.org}

\end_inset 

) tools for computational molecular biology.
 Python is an object oriented, interpreted, flexible language that is becoming
 increasingly popular for scientific computing.
 Python is easy to learn, has a very clear syntax and can easily be extended
 with modules written in C, C++ or FORTRAN.
\layout Standard

The Biopython web site (
\begin_inset LatexCommand \url{http://www.biopython.org}

\end_inset 

) provides an online resource for modules, scripts, and web links for developers
 of Python-based software for bioinformatics use and research.
 Basically, the goal of biopython is to make it as easy as possible to use
 python for bioinformatics by creating high-quality, reusable modules and
 classes.
 Biopython features include parsers for various Bioinformatics file formats
 (BLAST, Clustalw, FASTA, Genbank,...), access to online services (NCBI, Expasy,...),
 interfaces to common and not-so-common programs (Clustalw, DSSP, MSMS...),
 a standard sequence class, various clustering modules, a KD tree data structure
 etc.
 and even documentation.
 
\layout Standard

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.
\layout Section

Bio.PDB's installation
\layout Standard

Bio.PDB is automatically installed as part of Biopython.
 Biopython can be obtained from 
\begin_inset LatexCommand \url{http://www.biopython.org}

\end_inset 

.
 It runs on many platforms (Linux/Unix, windows, Mac,...).
\layout Section

Who's using Bio.PDB?
\layout Standard

Bio.PDB was used in the construction of DISEMBL, a web server that predicts
 disordered regions in proteins (
\begin_inset LatexCommand \url{http://dis.embl.de/}

\end_inset 

), and COLUMBA, a website that provides annotated protein structures (
\begin_inset LatexCommand \url{http://www.columba-db.de/}

\end_inset 

).
 Bio.PDB has also been used to perform a large scale search for active sites
 similarities between protein structures in the PDB (see 
\shape italic 
Proteins Struct.
 Func.
 Gen.
\shape default 
, 
\series bold 
2003
\series default 
, 51, 96-108), and to develop a new algorithm that identifies linear secondary
 structure elements (
\emph on 
BMC Bioinformatics
\emph default 
, 
\series bold 
2005
\series default 
, 6, 202, 
\begin_inset LatexCommand \url{http://www.biomedcentral.com/1471-2105/6/202}

\end_inset 

).
 
\layout Standard

Judging from requests for features and information, Bio.PDB is also used
 by several LPCs (Large Pharmaceutical Companies :-).
\layout Section

Is there a Bio.PDB reference?
\layout Standard

Yes, and I'd appreciate it if you would refer to Bio.PDB in publications
 if you make use of it.
 The reference is:
\layout Quote

Hamelryck, T., Manderick, B.
 (2003) PDB parser and structure class implemented in Python.
 
\shape italic 
Bioinformatics
\shape default 
, 
\series bold 
19
\series default 
, 2308-2310.
 
\layout Standard

The article can be freely downloaded via the Bioinformatics journal website
 (
\begin_inset LatexCommand \url{http://www.binf.ku.dk/users/thamelry/references.html}

\end_inset 

).
 I welcome e-mails telling me what you are using Bio.PDB for.
 Feature requests are welcome too.
\layout Section

How well tested is Bio.PDB?
\layout Standard

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.
\layout Section

How fast is it?
\layout Standard

The 
\family typewriter 
PDBParser
\family default 
 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.
\layout Section

Why should I use Bio.PDB?
\layout Standard

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.
 
\layout Section

Usage
\layout Subsection

General questions
\layout Subsubsection*

Importing Bio.PDB
\layout Standard

That's simple:
\layout LyX-Code

from Bio.PDB import *
\layout Subsubsection*

Is there support for molecular graphics?
\layout Standard

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:
\layout Itemize

PyMol: 
\begin_inset LatexCommand \url{http://pymol.sourceforge.net/}

\end_inset 


\layout Itemize

Chimera: 
\begin_inset LatexCommand \url{http://www.cgl.ucsf.edu/chimera/}

\end_inset 


\layout Itemize

PMV: 
\begin_inset LatexCommand \url{http://www.scripps.edu/~sanner/python/}

\end_inset 


\layout Itemize

Coot: 
\begin_inset LatexCommand \url{http://www.ysbl.york.ac.uk/~emsley/coot/}

\end_inset 


\layout Itemize

CCP4mg: 
\begin_inset LatexCommand \url{http://www.ysbl.york.ac.uk/~lizp/molgraphics.html}

\end_inset 


\layout Itemize

mmLib: 
\begin_inset LatexCommand \url{http://pymmlib.sourceforge.net/}

\end_inset 

 
\layout Itemize

VMD: 
\begin_inset LatexCommand \url{http://www.ks.uiuc.edu/Research/vmd/}

\end_inset 


\layout Itemize

MMTK: 
\begin_inset LatexCommand \url{http://starship.python.net/crew/hinsen/MMTK/}

\end_inset 


\layout Standard

I'd be crazy to write another molecular graphics application (been there
 - done that, actually :-).
\layout Subsection

Input/output
\layout Subsubsection*

How do I create a structure object from a PDB file?
\layout Standard

First, create a
\family typewriter 
 PDBParser 
\family default 
object:
\layout LyX-Code

parser=PDBParser()
\layout Standard

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):
\layout LyX-Code

structure=parser.get_structure('PHA-L', '1FAT.pdb')
\layout Subsubsection*

How do I create a structure object from an mmCIF file?
\layout Standard

Similarly to the case the case of PDB files, first create an 
\family typewriter 
MMCIFParser
\family default 
 object:
\layout LyX-Code

parser=MMCIFParser()
\layout Standard

Then use this parser to create a structure object from the mmCIF file:
\layout LyX-Code

structure=parser.get_structure('PHA-L', '1FAT.cif')
\layout Subsubsection*

...and what about the new PDB XML format?
\layout Standard

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 :-).
\layout Subsubsection*

I'd like to have some more low level access to an mmCIF file...
\layout Standard

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 
\family typewriter 
_atom_site.Cartn_y
\family default 
, 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:
\layout LyX-Code

mmcif_dict=MMCIF2Dict('1FAT.cif')
\layout Standard

Example: get the solvent content from an mmCIF file:
\layout LyX-Code

sc=mmcif_dict['_exptl_crystal.density_percent_sol']
\layout Standard

Example: get the list of the y coordinates of all atoms
\layout LyX-Code

y_list=mmcif_dict['_atom_site.Cartn_y']
\layout Subsubsection*

Can I access the header information?
\layout Standard

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.
 
\emph on 
Hence, if you are interested in the header information, it is a good idea
 to extract information from mmCIF files using the 
\family typewriter 
MMCIF2Dict
\family default 
 tool described above, instead of parsing the PDB header.
 
\layout Standard

Now that is clarified, let's return to parsing the PDB header.
 The structure object has an attribute called 
\family typewriter 
header
\family default 
 which is a python dictionary that maps header records to their values.
\layout Standard

Example:
\layout LyX-Code

resolution=structure.header['resolution']
\layout LyX-Code

keywords=structure.header['keywords']
\layout Standard

The available keys are 
\family typewriter 
name, head, deposition_\SpecialChar \-
date, release_\SpecialChar \-
date, structure_\SpecialChar \-
method, resolution,
 structure_\SpecialChar \-
reference 
\family default 
(maps to a list of references), 
\family typewriter 
journal_\SpecialChar \-
reference, author
\family default 
 and 
\family typewriter 
compound
\family default 
 (maps to a dictionary with various information about the crystallized compound).
\layout Standard

The dictionary can also be created without creating a 
\family typewriter 
Structure
\family default 
 object, ie.
 directly from the PDB file:
\layout LyX-Code

file=open(filename,'r')
\layout LyX-Code

header_dict=parse_pdb_header(file)
\layout LyX-Code

file.close()
\layout Subsubsection*

Can I use Bio.PDB with NMR structures (ie.
 with more than one model)?
\layout Standard

Sure.
 Many PDB parsers assume that there is only one model, making them all but
 useless for NMR structures.
 The design of the 
\family typewriter 
Structure
\family default 
 object makes it easy to handle PDB files with more than one model (see
 section 
\begin_inset LatexCommand \ref{sub:The-Structure-object}

\end_inset 

).
 
\layout Subsubsection*

How do I download structures from the PDB?
\layout Standard

This can be done using the 
\family typewriter 
PDBList
\family default 
 object, using the 
\family typewriter 
retrieve_pdb_file
\family default 
 method.
 The argument for this method is the PDB identifier of the structure.
\layout LyX-Code

pdbl=PDBList()
\layout LyX-Code

pdbl.retrieve_pdb_file('1FAT')
\layout Standard

The 
\family typewriter 
PDBList
\family default 
 class can also be used as a command-line tool: 
\layout LyX-Code

python PDBList.py 1fat
\layout Standard

The downloaded file will be called 
\family typewriter 
pdb1fat.ent
\family default 
 and stored in the current working directory.
 Note that the 
\family typewriter 
retrieve_pdb_file
\family default 
 method also has an optional argument 
\family typewriter 
pdir
\family default 
 that specifies a specific directory in which to store the downloaded PDB
 files.
 
\layout Standard

The 
\family typewriter 
retrieve_pdb_file
\family default 
 method also has some options to specify the compression format used for
 the download, and the program used for local decompression (default 
\family typewriter 
.Z
\family default 
 format and 
\family typewriter 
gunzip
\family default 
).
 In addition, the PDB ftp site can be specified upon creation of the 
\family typewriter 
PDBList
\family default 
 object.
 By default, the RCSB PDB server (
\begin_inset LatexCommand \url{ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/pdb/}

\end_inset 

) is used.
 See the API documentation for more details.
 Thanks again to Kristian Rother for donating this module.
\layout Subsubsection*

How do I download the entire PDB?
\layout Standard

The following commands will store all PDB files in the 
\family typewriter 
/data/pdb
\family default 
 directory: 
\layout LyX-Code

python PDBList.py all /data/pdb 
\layout LyX-Code

python PDBList.py all /data/pdb -d 
\layout Standard
\noindent 
The API method for this is called 
\family typewriter 
download_entire_pdb
\family default 
.
 Adding the 
\family typewriter 
-d
\family default 
 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.
 
\layout Subsubsection*

How do I keep a local copy of the PDB up-to-date?
\layout Standard

This can also be done using the 
\family typewriter 
PDBList
\family default 
 object.
 One simply creates a 
\family typewriter 
PDBList
\family default 
 object (specifying the directory where the local copy of the PDB is present)
 and calls the 
\family typewriter 
update_pdb
\family default 
 method:
\layout LyX-Code

pl=PDBList(pdb='/data/pdb')
\layout LyX-Code

pl.update_pdb()
\layout Standard

One can of course make a weekly 
\family typewriter 
cronjob 
\family default 
out of this to keep the local copy automatically up-to-date.
 The PDB ftp site can also be specified (see API documentation).
\layout Standard


\family typewriter 
PDBList
\family default 
 has some additional methods that can be of use.
 The 
\family typewriter 
get_all_obsolete
\family default 
 method can be used to get a list of all obsolete PDB entries.
 The 
\family typewriter 
changed_this_week
\family default 
 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 
\family typewriter 
PDBList
\family default 
, see the API documentation.
\layout Subsubsection*

What about all those buggy PDB files?
\layout Standard

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!
\layout Standard

Example:
\layout LyX-Code

# Permissive parser
\layout LyX-Code

parser=PDBParser(PERMISSIVE=1)
\layout LyX-Code

parser=PDBParser() # The same (default)
\layout LyX-Code

# Strict parser
\layout LyX-Code

strict_parser=PDBParser(PERMISSIVE=0)
\layout Standard

In the permissive state (DEFAULT), PDB files that obviously contain errors
 are 'corrected' (ie.
 some residues or atoms are left out).
 These errors include:
\layout Itemize

Multiple residues with the same identifier
\layout Itemize

Multiple atoms with the same identifier (taking into account the altloc
 identifier)
\layout Standard

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.
\layout Standard

Some errors however are automatically corrected.
 Normally each disordered atom should have a non-blanc 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.
\layout Standard

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.
\layout Subsubsection*

Can I write PDB files?
\layout Standard

Use the PDBIO class for this.
 It's easy to write out specific parts of a structure too, of course.
\layout Standard

Example: saving a structure
\layout LyX-Code

io=PDBIO()
\layout LyX-Code

io.set_structure(s)
\layout LyX-Code

io.save('out.pdb')
\layout Standard

If you want to write out a part of the structure, make use of the 
\family typewriter 
Select 
\family default 
class (also in 
\family typewriter 
PDBIO
\family default 
).
 Select has four methods:
\layout LyX-Code

accept_model(model)
\layout LyX-Code

accept_chain(chain)
\layout LyX-Code

accept_residue(residue)
\layout LyX-Code

accept_atom(atom)
\layout Standard

By default, every method returns 1 (which means the model/\SpecialChar \-
chain/\SpecialChar \-
residue/\SpecialChar \-
atom
 is included in the output).
 By subclassing 
\family typewriter 
Select
\family default 
 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:
\layout LyX-Code

class GlySelect(Select):
\layout LyX-Code

    def accept_residue(self, residue):
\layout LyX-Code

        if residue.get_name()=='GLY':
\layout LyX-Code

            return 1
\layout LyX-Code

        else:
\layout LyX-Code

            return 0
\layout LyX-Code

\layout LyX-Code

io=PDBIO()
\layout LyX-Code

io.set_structure(s)
\layout LyX-Code

io.save('gly_only.pdb', GlySelect())
\layout Standard

If this is all too complicated for you, the 
\family typewriter 
Dice 
\family default 
module contains a handy 
\family typewriter 
extract
\family default 
 function that writes out all residues in a chain between a start and end
 residue.
 
\layout Subsubsection*

Can I write mmCIF files?
\layout Standard

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.
\layout Subsection

The Structure object
\begin_inset LatexCommand \label{sub:The-Structure-object}

\end_inset 


\layout Subsubsection*

What's the overall layout of a Structure object?
\layout Standard

The 
\family typewriter 
Structure
\family default 
 object follows the so-called 
\family typewriter 
SMCRA
\family default 
 (Structure/\SpecialChar \-
Model/\SpecialChar \-
Chain/\SpecialChar \-
Residue/\SpecialChar \-
Atom) architecture : 
\layout Itemize

A structure consists of models
\layout Itemize

A model consists of chains
\layout Itemize

A chain consists of residues
\layout Itemize

A residue consists of atoms
\layout Standard

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 
\family typewriter 
Structure
\family default 
 object (forget about the 
\family typewriter 
Disordered
\family default 
 classes for now) is shown in Fig.
 
\begin_inset LatexCommand \ref{cap:SMCRA}

\end_inset 

.
\layout Standard


\begin_inset Float figure
placement tbh
wide false
collapsed false

\layout Standard
\align center 

\begin_inset Graphics
	filename images/smcra.png
	lyxscale 50
	width 100mm
	keepAspectRatio

\end_inset 


\layout Caption


\begin_inset LatexCommand \label{cap:SMCRA}

\end_inset 

UML diagram of SMCRA architecture of the 
\family typewriter 
Structure 
\family default 
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.
 
\end_inset 


\layout Subsubsection*

How do I navigate through a Structure object?
\layout Standard

The following code iterates through all atoms of a structure:
\layout LyX-Code

p=PDBParser()
\layout LyX-Code

structure=p.get_structure('X', 'pdb1fat.ent')
\layout LyX-Code

for model in structure:
\layout LyX-Code

  for chain in model: 
\layout LyX-Code

    for residue in chain:
\layout LyX-Code

      for atom in residue:
\layout LyX-Code

        print atom
\layout Standard

There are also some shortcuts:
\layout LyX-Code

# Iterate over all atoms in a structure
\layout LyX-Code

for atom in structure.get_atoms():
\layout LyX-Code

    print atom
\layout LyX-Code

# Iterate over all residues in a model
\layout LyX-Code

for residue in model.get_residues():
\layout LyX-Code

    print residue
\layout Standard

Structures, models, chains, residues and atoms are called 
\family typewriter 
Entities
\family default 
 in Biopython.
 You can always get a parent 
\family typewriter 
Entity
\family default 
 from a child 
\family typewriter 
Entity
\family default 
, eg.:
\layout LyX-Code

residue=atom.get_parent()
\layout LyX-Code

chain=residue.get_parent()
\layout Standard

You can also test wether an 
\family typewriter 
Entity
\family default 
 has a certain child using the 
\family typewriter 
has_id
\family default 
 method.
\layout Subsubsection*

Can I do that a bit more conveniently?
\layout Standard

You can do things like:
\layout LyX-Code

atoms=structure.get_atoms()
\layout LyX-Code

residue=structure.get_residues()
\layout LyX-Code

atoms=chain.get_atoms()
\layout Standard

You can also use the 
\family typewriter 
Selection.unfold_entities
\family default 
 function:
\layout LyX-Code

# Get all residues from a structure
\layout LyX-Code

res_list=Selection.unfold_entities(structure, 'R')
\layout LyX-Code

# Get all atoms from a chain
\layout LyX-Code

atom_list=Selection.unfold_entities(chain, 'A')
\layout Standard

Obviously, 
\family typewriter 
A=atom, R=residue, C=chain, M=model, S=structure
\family default 
.
 You can use this to go up in the hierarchy, eg.
\begin_inset ERT
status Collapsed

\layout Standard

\backslash 

\end_inset 

 to get a list of (unique) 
\family typewriter 
Residue
\family default 
 or 
\family typewriter 
Chain
\family default 
 parents from a list of 
\family typewriter 
Atoms
\family default 
:
\layout LyX-Code

residue_list=Selection.unfold_entities(atom_list, 'R')
\layout LyX-Code

chain_list=Selection.unfold_entities(atom_list, 'C')
\layout Standard

For more info, see the API documentation.
\layout Subsubsection*

How do I extract a specific 
\family typewriter 
Atom/\SpecialChar \-
Residue/\SpecialChar \-
Chain/\SpecialChar \-
Model
\family default 
 from a Structure?
\layout Standard

Easy.
 Here are some examples:
\layout LyX-Code

model=structure[0]
\layout LyX-Code

chain=model['A']
\layout LyX-Code

residue=chain[100]
\layout LyX-Code

atom=residue['CA']
\layout Standard

Note that you can use a shortcut:
\layout LyX-Code

atom=structure[0]['A'][100]['CA']
\layout Subsubsection*

What is a model id?
\layout Standard

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.
\layout Subsubsection*

What is a chain id?
\layout Standard

The chain id is specified in the PDB/mmCIF file, and is a single character
 (typically a letter).
 
\layout Subsubsection*

What is a residue id?
\layout Standard

This is a bit more complicated, due to the clumsy PDB format.
 A residue id is a tuple with three elements:
\layout Itemize

The 
\series bold 
hetero-flag
\series default 
: this is
\family typewriter 
 'H_'
\family default 
 plus the name of the hetero-residue (eg.

\family typewriter 
 'H_GLC'
\family default 
 in the case of a glucose molecule), or 
\family typewriter 
'W'
\family default 
 in the case of a water molecule.
\layout Itemize

The 
\series bold 
sequence identifier
\series default 
 in the chain, eg.
 100
\layout Itemize

The 
\series bold 
insertion code
\series default 
, eg.
 'A'.
 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.
\layout Standard

The id of the above glucose residue would thus be 
\family typewriter 
('H_GLC', 100, 'A')
\family default 
.
 If the hetero-flag and insertion code are blanc, the sequence identifier
 alone can be used:
\layout LyX-Code

# Full id
\layout LyX-Code

residue=chain[(' ', 100, ' ')]
\layout LyX-Code

# Shortcut id
\layout LyX-Code

residue=chain[100]
\layout Standard

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.
 
\layout Subsubsection*

What is an atom id?
\layout Standard

The atom id is simply the atom name (eg.
 
\family typewriter 
'CA'
\family default 
).
 In practice, the atom name is created by stripping all spaces from the
 atom name in the PDB file.
 
\layout Standard

However, in PDB files, a space can be part of an atom name.
 Often, calcium atoms are called 
\family typewriter 
'CA..'
\family default 
 in order to distinguish them from C
\begin_inset Formula $\alpha$
\end_inset 

 atoms (which are called 
\family typewriter 
'.CA.'
\family default 
).
 In cases were stripping the spaces would create problems (ie.
 two atoms called
\family typewriter 
 'CA'
\family default 
 in the same residue) the spaces are kept.
\layout Subsubsection*

How is disorder handled?
\layout Standard

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).
 
\layout Standard

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 C
\begin_inset Formula $\alpha$
\end_inset 

 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.
\layout Standard


\series bold 
Disordered atom positions
\series default 
 are represented by ordinary 
\family typewriter 
Atom
\family default 
 objects, but all 
\family typewriter 
Atom
\family default 
 objects that represent the same physical atom are stored in a 
\family typewriter 
Disordered\SpecialChar \-
Atom
\family default 
 object (see Fig.
 
\begin_inset LatexCommand \ref{cap:SMCRA}

\end_inset 

).
 Each 
\family typewriter 
Atom
\family default 
 object in a 
\family typewriter 
Disordered\SpecialChar \-
Atom
\family default 
 object can be uniquely indexed using its altloc specifier.
 The 
\family typewriter 
Disordered\SpecialChar \-
Atom
\family default 
 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 
\family typewriter 
Atom 
\family default 
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.
\layout Standard

Each disordered atom has a characteristic altloc identifier.
 You can specify that a 
\family typewriter 
Disordered\SpecialChar \-
Atom
\family default 
 object should behave like the 
\family typewriter 
Atom
\family default 
 object associated with a specific altloc identifier:
\layout LyX-Code

atom.disordered_select('A') # select altloc A atom
\layout LyX-Code

atom.disordered_select('B') # select altloc B atom 
\layout Standard

A special case arises when disorder is due to 
\series bold 
point mutations
\series default 
, 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.
\layout Standard

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 
\family typewriter 
Residue
\family default 
 object as in the common case.
 In this case, each residue is represented by one 
\family typewriter 
Residue
\family default 
 object, and both 
\family typewriter 
Residue
\family default 
 objects are stored in a single 
\family typewriter 
Disordered\SpecialChar \-
Residue
\family default 
 object (see Fig.
 
\begin_inset LatexCommand \ref{cap:SMCRA}

\end_inset 

).
\layout Standard

The 
\family typewriter 
Dis\SpecialChar \-
ordered\SpecialChar \-
Residue
\family default 
 object forwards all un\SpecialChar \-
caught methods to the selected 
\family typewriter 
Residue
\family default 
 object (by default the last 
\family typewriter 
Residue
\family default 
 object added), and thus behaves like an ordinary residue.
 Each 
\family typewriter 
Residue
\family default 
 object in a 
\family typewriter 
Disordered\SpecialChar \-
Residue
\family default 
 object can be uniquely identified by its residue name.
 In the above example, residue Ser 60 would have id 'SER' in the 
\family typewriter 
Disordered\SpecialChar \-
Residue
\family default 
 object, while residue Cys 60 would have id 'CYS'.
 The user can select the active 
\family typewriter 
Residue
\family default 
 object in a 
\family typewriter 
Disordered\SpecialChar \-
Residue
\family default 
 object via this id.
\layout Standard

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.
\layout LyX-Code

residue=chain[10]
\layout LyX-Code

residue.disordered_select('CYS')
\layout Standard

In addition, you can get a list of all 
\family typewriter 
Atom
\family default 
 objects (ie.
 all 
\family typewriter 
DisorderedAtom
\family default 
 objects are 'unpacked' to their individual 
\family typewriter 
Atom
\family default 
 objects) using the 
\family typewriter 
get_unpacked_list
\family default 
 method of a 
\family typewriter 
(Disordered)\SpecialChar \-
Residue
\family default 
 object.
\layout Subsubsection*

Can I sort residues in a chain somehow?
\layout Standard

Yes, kinda, but I'm waiting for a request for this feature to finish it
 :-).
\layout Subsubsection*

How are ligands and solvent handled?
\layout Standard

See 'What is a residue id?'.
\layout Subsubsection*

What about B factors?
\layout Standard

Well, yes! Bio.PDB supports isotropic and anisotropic B factors, and also
 deals with standard deviations of anisotropic B factor if present (see
 
\begin_inset LatexCommand \ref{sub:Analysis}

\end_inset 

).
\layout Subsubsection*

What about standard deviation of atomic positions?
\layout Standard

Yup, supported.
 See section 
\begin_inset LatexCommand \ref{sub:Analysis}

\end_inset 

.
\layout Subsubsection*

I think the SMCRA data structure is not flexible/\SpecialChar \-
sexy/\SpecialChar \-
whatever enough...
\layout Standard

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.
\layout Standard

Moreover, it is quite easy to build more specialised data structures on
 top of the 
\family typewriter 
Structure
\family default 
 class (eg.
 there's a 
\family typewriter 
Polypeptide
\family default 
 class).
 On the other hand, the 
\family typewriter 
Structure 
\family default 
object is built using a Parser/\SpecialChar \-
Consumer approach (called 
\family typewriter 
PDBParser/\SpecialChar \-
MMCIFParser
\family default 
 and 
\family typewriter 
Structure\SpecialChar \-
Builder
\family default 
, respectively).
 One can easily re-use the PDB/mmCIF parsers by implementing a specialised
 
\family typewriter 
Structure\SpecialChar \-
Builder
\family default 
 class.
 It is of course also trivial to add support for new file formats by writing
 new parsers.
\layout Subsection


\begin_inset LatexCommand \label{sub:Analysis}

\end_inset 

Analysis
\layout Subsubsection*

How do I extract information from an 
\family typewriter 
Atom
\family default 
 object?
\layout Standard

Using the following methods:
\layout LyX-Code

a.get_name() # atom name (spaces stripped, e.g.
 'CA')
\layout LyX-Code

a.get_id() # id (equals atom name)
\layout LyX-Code

a.get_coord() # atomic coordinates
\layout LyX-Code

a.get_vector() # atomic coordinates as Vector object
\layout LyX-Code

a.get_bfactor() # isotropic B factor
\layout LyX-Code

a.get_occupancy() # occupancy
\layout LyX-Code

a.get_altloc() # alternative location specifier
\layout LyX-Code

a.get_sigatm() # std.
 dev.
 of atomic parameters
\layout LyX-Code

a.get_siguij() # std.
 dev.
 of anisotropic B factor
\layout LyX-Code

a.get_anisou() # anisotropic B factor
\layout LyX-Code

a.get_fullname() # atom name (with spaces, e.g.
 '.CA.')
\layout Subsubsection*

How do I extract information from a 
\family typewriter 
Residue
\family default 
 object?
\layout Standard

Using the following methods:
\layout LyX-Code

r.get_resname() # return the residue name (eg.
 'GLY')
\layout LyX-Code

r.is_disordered() # 1 if the residue has disordered atoms
\layout LyX-Code

r.get_segid() # return the SEGID
\layout LyX-Code

r.has_id(name) # test if a residue has a certain atom
\layout Subsubsection*

How do I measure distances?
\layout Standard

That's simple: the minus operator for atoms has been overloaded to return
 the distance between two atoms.
 
\layout Standard

Example:
\layout LyX-Code

# Get some atoms
\layout LyX-Code

ca1=residue1['CA']
\layout LyX-Code

ca2=residue2['CA']
\layout LyX-Code

# Simply subtract the atoms to get their distance
\layout LyX-Code

distance=ca1-ca2
\layout Subsubsection*

How do I measure angles?
\layout Standard

This can easily be done via the vector representation of the atomic coordinates,
 and the 
\family typewriter 
calc_angle
\family default 
 function from the 
\family typewriter 
Vector
\family default 
 module:
\layout LyX-Code

vector1=atom1.get_vector()
\layout LyX-Code

vector2=atom2.get_vector()
\layout LyX-Code

vector3=atom3.get_vector()
\layout LyX-Code

angle=calc_angle(vector1, vector2, vector3)
\layout Subsubsection*

How do I measure torsion angles?
\layout Standard

Again, this can easily be done via the vector representation of the atomic
 coordinates, this time using the 
\family typewriter 
calc_dihedral
\family default 
 function from the 
\family typewriter 
Vector
\family default 
 module:
\layout LyX-Code

vector1=atom1.get_vector()
\layout LyX-Code

vector2=atom2.get_vector()
\layout LyX-Code

vector3=atom3.get_vector()
\layout LyX-Code

vector4=atom4.get_vector()
\layout LyX-Code

angle=calc_dihedral(vector1, vector2, vector3, vector4)
\layout Subsubsection*

How do I determine atom-atom contacts?
\layout Standard

Use 
\family typewriter 
NeighborSearch
\family default 
.
 This uses a KD tree data structure coded in C++ behind the screens, so
 it's pretty darn fast (see 
\family typewriter 
Bio.KDTree
\family default 
).
\layout Subsubsection*

How do I extract polypeptides from a 
\family typewriter 
Structure
\family default 
 object?
\layout Standard

Use 
\family typewriter 
PolypeptideBuilder
\family default 
.
 You can use the resulting 
\family typewriter 
Polypeptide
\family default 
 object to get the sequence as a 
\family typewriter 
Seq
\family default 
 object or to get a list of C
\begin_inset Formula $\alpha$
\end_inset 

 atoms as well.
 Polypeptides can be built using a C-N or a C
\begin_inset Formula $\alpha$
\end_inset 

-C
\begin_inset Formula $\alpha$
\end_inset 

 distance criterion.
\layout Standard

Example:
\layout LyX-Code

# Using C-N 
\layout LyX-Code

ppb=PPBuilder()
\layout LyX-Code

for pp in ppb.build_peptides(structure): 
\layout LyX-Code

    print pp.get_sequence()
\layout LyX-Code

# Using CA-CA
\layout LyX-Code

ppb=CaPPBuilder()
\layout LyX-Code

for pp in ppb.build_peptides(structure): 
\layout LyX-Code

    print pp.get_sequence()
\layout Standard

Note that in the above case only model 0 of the structure is considered
 by 
\family typewriter 
PolypeptideBuilder
\family default 
.
 However, it is possible to use 
\family typewriter 
PolypeptideBuilder
\family default 
 to build 
\family typewriter 
Polypeptide
\family default 
 objects from 
\family typewriter 
Model
\family default 
 and 
\family typewriter 
Chain
\family default 
 objects as well.
\layout Subsubsection*

How do I get the sequence of a structure?
\layout Standard

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 
\family typewriter 
Polypeptide 
\family default 
objects.
 The sequence is represented as a Biopython 
\family typewriter 
Seq 
\family default 
object, and its alphabet is defined by a 
\family typewriter 
ProteinAlphabet 
\family default 
object.
\layout Standard

Example:
\layout LyX-Code

>>> seq=polypeptide.get_sequence()
\layout LyX-Code

>>> print seq
\layout LyX-Code

Seq('SNVVE...', <class Bio.Alphabet.ProteinAlphabet>)
\layout Subsubsection*

How do I determine secondary structure?
\layout Standard

For this functionality, you need to install DSSP (and obtain a license for
 it - free for academic use, see 
\begin_inset LatexCommand \url{http://www.cmbi.kun.nl/gv/dssp/}

\end_inset 

).
 Then use the 
\family typewriter 
DSSP
\family default 
 class, which maps 
\family typewriter 
Residue
\family default 
 objects to their secondary structure (and accessible surface area).
 The DSSP codes are listed in Table 
\begin_inset LatexCommand \ref{cap:DSSP-codes}

\end_inset 

.
 Note that DSSP (the program, and thus by consequence the class) cannot
 handle multiple models!
\layout Standard


\begin_inset Float table
wide false
collapsed false

\layout Subsubsection*


\begin_inset  Tabular
<lyxtabular version="3" rows="9" columns="2">
<features>
<column alignment="center" valignment="top" leftline="true" width="0">
<column alignment="center" valignment="top" leftline="true" rightline="true" width="0">
<row topline="true" bottomline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\layout Standard

Code
\end_inset 
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\layout Standard

Secondary structure
\end_inset 
</cell>
</row>
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\layout Standard

H
\end_inset 
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\layout Standard


\begin_inset Formula $\alpha$
\end_inset 

-helix
\end_inset 
</cell>
</row>
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\layout Standard

B
\end_inset 
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\layout Standard


\family roman 
\series medium 
\shape up 
\size normal 
\emph off 
\bar no 
\noun off 
\color none
Isolated 
\family default 
\series default 
\shape default 
\size default 
\emph default 
\bar default 
\noun default 
\color default

\begin_inset Formula $\beta$
\end_inset 


\family roman 
\series medium 
\shape up 
\size normal 
\emph off 
\bar no 
\noun off 
\color none
-bridge resid
\family default 
\series default 
\shape default 
\size default 
\emph default 
\bar default 
\noun default 
\color default
ue
\end_inset 
</cell>
</row>
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\layout Standard

E
\end_inset 
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\layout Standard


\family roman 
\series medium 
\shape up 
\size normal 
\emph off 
\bar no 
\noun off 
\color none
Strand 
\end_inset 
</cell>
</row>
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\layout Standard

G
\end_inset 
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\layout Standard


\family roman 
\series medium 
\shape up 
\size normal 
\emph off 
\bar no 
\noun off 
\color none
3-10 helix 
\end_inset 
</cell>
</row>
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\layout Standard

I
\end_inset 
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\layout Standard


\begin_inset Formula $\Pi$
\end_inset 

-
\family roman 
\series medium 
\shape up 
\size normal 
\emph off 
\bar no 
\noun off 
\color none
helix 
\end_inset 
</cell>
</row>
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\layout Standard

T
\end_inset 
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\layout Standard


\family roman 
\series medium 
\shape up 
\size normal 
\emph off 
\bar no 
\noun off 
\color none
Turn
\end_inset 
</cell>
</row>
<row topline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\layout Standard

S
\end_inset 
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\layout Standard


\family roman 
\series medium 
\shape up 
\size normal 
\emph off 
\bar no 
\noun off 
\color none
Bend 
\end_inset 
</cell>
</row>
<row topline="true" bottomline="true">
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text

\layout Standard

-
\end_inset 
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text

\layout Standard


\family roman 
\series medium 
\shape up 
\size normal 
\emph off 
\bar no 
\noun off 
\color none
Other
\end_inset 
</cell>
</row>
</lyxtabular>

\end_inset 


\layout Caption


\begin_inset LatexCommand \label{cap:DSSP-codes}

\end_inset 

DSSP codes in Bio.PDB.
\end_inset 


\layout Subsubsection*

How do I calculate the accessible surface area of a residue?
\layout Standard

Use the 
\family typewriter 
DSSP 
\family default 
class (see also previous entry).
 But see also next entry.
\layout Subsubsection*

How do I calculate residue depth?
\layout Standard

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
 (
\begin_inset LatexCommand \url{http://www.scripps.edu/pub/olson-web/people/sanner/html/msms_home.html}

\end_inset 

).
 Then use the 
\family typewriter 
ResidueDepth
\family default 
 class.
 This class behaves as a dictionary which maps 
\family typewriter 
Residue
\family default 
 objects to corresponding (residue depth, C
\begin_inset Formula $\alpha$
\end_inset 

 depth) tuples.
 The C
\begin_inset Formula $\alpha$
\end_inset 

 depth is the distance of a residue's C
\begin_inset Formula $\alpha$
\end_inset 

 atom to the solvent accessible surface.
 
\layout Standard

Example:
\layout LyX-Code

model=structure[0]
\layout LyX-Code

rd=ResidueDepth(model, pdb_file)
\layout LyX-Code

residue_depth, ca_depth=rd[some_residue]
\layout Standard

You can also get access to the molecular surface itself (via the 
\family typewriter 
get_surface
\family default 
 function), in the form of a Numeric python array with the surface points.
\layout Subsubsection*

How do I calculate Half Sphere Exposure?
\layout Standard

Half Sphere Exposure (HSE) is a new, 2D measure of solvent exposure.
 Basically, it counts the number of C
\begin_inset Formula $\alpha$
\end_inset 

 atoms around a residue in the direction of its side chain, and in the opposite
 direction (within a radius of 13 ).
 Despite its simplicity, it outperforms many other measures of solvent exposure.
 An article describing this novel 2D measure has been submitted.
\layout Standard

HSE comes in two flavors: HSE
\begin_inset Formula $\alpha$
\end_inset 

 and HSE
\begin_inset Formula $\beta$
\end_inset 

.
 The former only uses the C
\begin_inset Formula $\alpha$
\end_inset 

 atom positions, while the latter uses the C
\begin_inset Formula $\alpha$
\end_inset 

 and C
\begin_inset Formula $\beta$
\end_inset 

 atom positions.
 The HSE measure is calculated by the 
\family typewriter 
HSExposure
\family default 
 class, which can also calculate the contact number.
 The latter class has methods which return dictionaries that map a 
\family typewriter 
Residue
\family default 
 object to its corresponding HSE
\begin_inset Formula $\alpha$
\end_inset 

, HSE
\begin_inset Formula $\beta$
\end_inset 

 and contact number values.
\layout Standard

Example:
\layout LyX-Code

model=structure[0]
\layout LyX-Code

hse=HSExposure()
\layout LyX-Code

# Calculate HSEalpha
\layout LyX-Code

exp_ca=hse.calc_hs_exposure(model, option='CA3')
\layout LyX-Code

# Calculate HSEbeta
\layout LyX-Code

exp_cb=hse.calc_hs_exposure(model, option='CB')
\layout LyX-Code

# Calculate classical coordination number exp_fs=hse.calc_fs_exposure(model)
\layout LyX-Code

# Print HSEalpha for a residue
\layout LyX-Code

print exp_ca[some_residue]
\layout Subsubsection*

How do I map the residues of two related structures onto each other?
\layout Standard

First, create an alignment file in FASTA format, then use the 
\family typewriter 
StructureAlignment
\family default 
 class.
 This class can also be used for alignments with more than two structures.
\layout Subsubsection*

How do I test if a Residue object is an amino acid?
\layout Standard

Use 
\family typewriter 
is_aa(residue)
\family default 
.
\layout Subsubsection*

Can I do vector operations on atomic coordinates?
\layout Standard


\family typewriter 
Atom
\family default 
 objects return a 
\family typewriter 
Vector
\family default 
 object representation of the coordinates with the 
\family typewriter 
get_vector
\family default 
 method.
 
\family typewriter 
Vector
\family default 
 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.
\layout Subsubsection*

How do I put a virtual C
\begin_inset Formula $\beta$
\end_inset 

 on a Gly residue?
\layout Standard

OK, I admit, this example is only present to show off the possibilities
 of Bio.PDB's 
\family typewriter 
Vector
\family default 
 module (though this code is actually used in the 
\family typewriter 
HSExposure
\family default 
 module, which contains a novel way to parametrize residue exposure - publicatio
n underway).
 Suppose that you would like to find the position of a Gly residue's C
\begin_inset Formula $\beta$
\end_inset 

 atom, if it had one.
 How would you do that? Well, rotating the N atom of the Gly residue along
 the C
\begin_inset Formula $\alpha$
\end_inset 

-C bond over -120 degrees roughly puts it in the position of a virtual C
\begin_inset Formula $\beta$
\end_inset 

 atom.
 Here's how to do it, making use of the 
\family typewriter 
rotaxis
\family default 
 method (which can be used to construct a rotation around a certain axis)
 of the 
\family typewriter 
Vector
\family default 
 module:
\layout LyX-Code

# get atom coordinates as vectors
\layout LyX-Code

n=residue['N'].get_vector() 
\layout LyX-Code

c=residue['C'].get_vector() 
\layout LyX-Code

ca=residue['CA'].get_vector()
\layout LyX-Code

# center at origin
\layout LyX-Code

n=n-ca 
\layout LyX-Code

c=c-ca 
\layout LyX-Code

# find rotation matrix that rotates n 
\layout LyX-Code

# -120 degrees along the ca-c vector
\layout LyX-Code

rot=rotaxis(-pi*120.0/180.0, c)
\layout LyX-Code

# apply rotation to ca-n vector
\layout LyX-Code

cb_at_origin=n.left_multiply(rot)
\layout LyX-Code

# put on top of ca atom
\layout LyX-Code

cb=cb_at_origin+ca
\layout Standard

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 
\family typewriter 
**
\family default 
), and dot (use 
\family typewriter 
*
\family default 
) product, angle, norm, etc.) and the above mentioned 
\family typewriter 
rotaxis
\family default 
 function, the 
\family typewriter 
Vector
\family default 
 module also has methods to rotate (
\family typewriter 
rotmat
\family default 
) or reflect (
\family typewriter 
refmat
\family default 
) one vector on top of another.
\layout Subsection

Manipulating the structure
\layout Subsubsection*

How do I superimpose two structures?
\layout Standard

Surprisingly, this is done using the 
\family typewriter 
Superimposer
\family default 
 object.
 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 
\family typewriter 
Superimposer
\family default 
 object can also apply the rotation/translation to a list of atoms.
 The rotation and translation are stored as a tuple in the 
\family typewriter 
rotran
\family default 
 attribute of the 
\family typewriter 
Superimposer
\family default 
 object (note that the rotation is right multiplying!).
 The RMSD is stored in the 
\family typewriter 
rmsd
\family default 
 attribute.
\layout Standard

The algorithm used by 
\family typewriter 
Superimposer
\family default 
 comes from 
\shape italic 
Matrix computations, 2nd ed.
 Golub, G.
 & Van Loan (1989)
\shape default 
 and makes use of singular value decomposition (this is implemented in the
 general 
\family typewriter 
Bio.\SpecialChar \-
SVDSuperimposer
\family default 
 module).
\layout Standard

Example:
\layout LyX-Code

sup=Superimposer()
\layout LyX-Code

# Specify the atom lists
\layout LyX-Code

# 'fixed' and 'moving' are lists of Atom objects
\layout LyX-Code

# The moving atoms will be put on the fixed atoms
\layout LyX-Code

sup.set_atoms(fixed, moving)
\layout LyX-Code

# Print rotation/translation/rmsd
\layout LyX-Code

print sup.rotran
\layout LyX-Code

print sup.rms 
\layout LyX-Code

# Apply rotation/translation to the moving atoms
\layout LyX-Code

sup.apply(moving)
\layout Subsubsection*

How do I superimpose two structures based on their active sites?
\layout Standard

Pretty easily.
 Use the active site atoms to calculate the rotation/translation matrices
 (see above), and apply these to the whole molecule.
\layout Subsubsection*

Can I manipulate the atomic coordinates?
\layout Standard

Yes, using the 
\family typewriter 
transform
\family default 
 method of the 
\family typewriter 
Atom
\family default 
 object, or directly using the 
\family typewriter 
set_coord
\family default 
 method.
\layout Section

Other Structural Bioinformatics modules
\layout Subsubsection*

Bio.SCOP
\layout Standard

Info coming soon.
\layout Subsubsection*

Bio.FSSP
\layout Standard

Info coming soon.
\layout Section

You haven't answered my question yet!
\layout Standard

Woah! It's late and I'm tired, and a glass of excellent 
\shape italic 
Pedro Ximenez
\shape default 
 sherry is waiting for me.
 Just drop me a mail, and I'll answer you in the morning (with a bit of
 luck...).
\layout Section

Contributors
\layout Standard

The main author/maintainer of Bio.PDB is yours truly.
 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
 
\family typewriter 
Polypeptide 
\family default 
module.
 Many thanks to Brad Chapman, Jeffrey Chang, Andrew Dalke and Iddo Friedberg
 for suggestions, comments, help and/or biting criticism :-).
\layout Section

Can I contribute?
\layout Standard

Yes, yes, yes! Just send me an e-mail (thamelry@binf.ku.dk) if you have something
 useful to contribute! Eternal fame awaits!
\layout Section

Biopython License Agreement
\layout Standard

Permission to use, copy, modify, and distribute this software and its documentat
ion with or without modifications and for any purpose and without fee is
 hereby granted, provided that any copyright notices appear in all copies
 and that both those copyright notices and this permission notice appear
 in supporting documentation, and that the names of the contributors or
 copyright holders not be used in advertising or publicity pertaining to
 distribution of the software without specific prior permission.
\layout Standard

THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES
 WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILI
TY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS
 BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
 WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION
 OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN
 CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
 
\the_end