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| − | == Introduction ==
| + | [[Image:cealign_ex1.png|300px|thumb|right|cealign superposition of 1c0mB and 1bco]] |
| | | | |
| − | '''Go directly to [[Cealign#Version_0.8-RBS|DOWNLOAD]]'''
| + | [[cealign]] aligns two proteins using the CE algorithm. It is very robust for proteins with little to no sequence similarity (twilight zone). For proteins with decent structural similarity, the [[super]] command is preferred and with decent sequence similarity, the [[align]] command is preferred, because these commands are much faster than [[cealign]]. |
| | | | |
| − | This page is the home page of the open-source CEAlign PyMOL plugin. The CE algorithm is a fast and accurate protein structure alignment algorithm, pioneered by Drs. Shindyalov and Bourne (See | + | ''This command is new in PyMOL 1.3, see the [[cealign plugin]] for manual installation.'' |
| − | References). There are a few changes from the original CE publication (See Notes).
| |
| | | | |
| − | The source code is implemented in C with the rotations finally done by Numpy in Python. Because the computationally complex portion of the code is written in C, it's quick. That is, on my machines --- relatively fast 64-bit machines --- I can align two 400+ amino acid structures in about 0.300 s with the C++ implementation.
| + | == Usage == |
| | | | |
| − | This plugs into PyMol very easily. See [[Cealign#The_Code|the code]] and [[Cealign#Examples|examples]] for installation and usage.
| + | cealign target, mobile [, target_state [, mobile_state |
| | + | [, quiet [, guide [, d0 [, d1 [, window [, gap_max |
| | + | [, transform [, object ]]]]]]]]]] |
| | | | |
| − | == Comparison to PyMol == | + | == Arguments == |
| − | '''Why should you use this?'''
| |
| | | | |
| − | PyMOL's structure alignment algorithm is fast and robust. However, its first step is to perform a sequence alignment of the two selections. Thus, proteins in the '''twilight zone''' or those having a low sequence identity, may not align well. Because CE is a structure-based alignment, this is not a problem. Consider the following example. The image at LEFT was the result of CE-aligning two proteins (1C0M chain B to 1BCO). The result is '''152''' aligned (alpha carbons) residues (not atoms) at '''4.96 Angstroms'''. The image on the RIGHT shows the results from PyMol's align command: an alignment of '''221 atoms''' (not residues) at an RMSD of '''15.7 Angstroms'''.
| + | '''Note''': The '''mobile''' and '''target''' arguments are swapped with respect to the [[align]] and [[super]] commands. |
| | | | |
| − | <gallery>
| + | * '''target''' = string: atom selection of target object |
| − | Image:cealign_ex1.png|Cealign's results (152 aligned; 4.96 Ang.)
| + | * '''mobile''' = string: atom selection of mobile object |
| − | Image:pymol_align.png|PyMol's results (763 atoms; 18.4 Ang. )
| + | * '''target_state''' = int: object state of target selection {default: 1} |
| − | </gallery>
| + | * '''mobile_state''' = int: object state of mobile selection {default: 1} |
| | + | * '''quiet''' = 0/1: suppress output {default: 0 in command mode, 1 in API} |
| | + | * '''guide''' = 0/1: only use "guide" atoms (CA, C4') {default: 1} |
| | + | * '''d0, d1, window, gap_max''': CE algorithm parameters |
| | + | * '''transform''' = 0/1: do superposition {default: 1} |
| | + | * '''object''' = string: name of alignment object to create {default: (no alignment object)} |
| | | | |
| − | == Examples == | + | == Example == |
| − | === Usage ===
| |
| − | ==== Syntax ====
| |
| | | | |
| − | CEAlign has the semantic, and syntactic formalism of
| + | <syntaxhighlight lang="python"> |
| − | <source lang="python"> | + | fetch 1c0mB 1bco, async=0 |
| − | cealign MASTER, TARGET
| + | as ribbon |
| − | </source>
| + | cealign 1bco, 1c0mB, object=aln |
| − | where a post-condition of the algorithm is that the coordinates of the '''MASTER''' protein are unchanged. This allows for easier multi-protein alignments. For example,
| + | </syntaxhighlight> |
| − | <source lang="python">
| |
| − | cealign 1AUE, 1BZ4
| |
| − | cealign 1AUE, 1B68
| |
| − | cealign 1AUE, 1A7V
| |
| − | cealign 1AUE, 1CPR
| |
| − | </source> | |
| − | will superimpose all the TARGETS onto the MASTER.
| |
| | | | |
| − | =====Examples===== | + | == See Also == |
| − | <source lang="python">
| |
| − | cealign 1cll and i. 42-55, 1ggz and c. A
| |
| − | cealign 1kao, 1ctq
| |
| − | cealign 1fao, 1eaz
| |
| − | </source>
| |
| | | | |
| − | =====Multiple Structure Alignments=====
| + | * [[super]] |
| − | Use the '''alignto''' command, now provided with cealign. Just type,
| + | * [[align]] |
| − | <source lang="python">
| + | * [[cealign plugin]] |
| − | alignto PROT
| |
| − | </source>
| |
| − | to align all your proteins in PyMOL to the one called, '''PROT'''.
| |
| | | | |
| − | | + | [[Category:Commands|Align]] |
| − | | + | [[Category:Structure_Alignment|Align]] |
| − | === Results ===
| |
| − | See '''Changes''' for updates. But, overall, the results here are great.
| |
| − | | |
| − | <gallery>
| |
| − | Image:v7_1fao_1eaz.png|EASY: 1FAO vs. 1EAZ; 96 residues, 1.28 Ang
| |
| − | Image:v7_1cbs_1hmt.png|EASY: 1CBS vs. 1HMT; 128 residues, 2.01 Ang
| |
| − | Image:v7_1a15_1b50.png|MODERATE: 1A15 vs 1B50; 56 residues, 2.54 Ang.
| |
| − | Image:v7_1oan_1s6n.png|EASY: 1OAN vs. 1S6N (state 1); 96 residues aligned to 3.83 Ang. RMSD.
| |
| − | Image:v7_1rlw_1byn.png|HARD: 1RLW to 1BYN; 104 residues; 2.21 Ang.
| |
| − | Image:v7_1ten_3hhr.png|HARD: 1TEN vs. 3HHR; 80 residues, 2.91 Ang.
| |
| − | Image:v7_2sim_1nsb.png|HARD: 2SIM vs. 1NSB; 272 residues, 4.93 Ang.
| |
| − | Image:v7_1cew_1mol.png|HARD: 1CEW vs. 1MOL; 80 residues, 4.03 Ang.
| |
| − | </gallery>
| |
| − | | |
| − | == Installation ==
| |
| − | ===Windows systems===
| |
| − | This is a quick and dirty method to get it working on Win32 right now, more details coming soon.
| |
| − | ====Requirements====
| |
| − | * Latest PyMol, installed on your system
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| − | * Numpy for python 2.4; quick download of just what's needed: http://users.umassmed.edu/Shivender.Shandilya/pymol/numpy.zip
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| − | * Pre-compiled ccealign.pyd python module: http://users.umassmed.edu/Shivender.Shandilya/pymol/ccealign.zip
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| − | * Modified pymolrc: http://users.umassmed.edu/Shivender.Shandilya/pymol/pymolrc
| |
| − | * cealign.py and qkabsch.py from the Cealign-0.8-RBS package: download below
| |
| − | | |
| − | ====Directions====
| |
| − | # Unzip the numpy.zip file, which will give you a folder named '''numpy'''
| |
| − | # Move this entire folder to: C:\Program Files\DeLano Scientific\PyMOL\modules\ (or the corresponding location on your system)
| |
| − | # Unzip ccealign.zip, which will give you a file called '''ccealign.pyd'''
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| − | # Move this pyd file to: C:\Program Files\DeLano Scientific\PyMOL\py24\DLLs\ (or the corresponding location on your system)
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| − | # Copy the downloaded '''pymolrc''' file to: C:\Program Files\DeLano Scientific\PyMOL\ (or the corresponding location on your system)
| |
| − | # Run PyMol and load some molecules
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| − | # Run this command in Pymol: '''cealign molecule1, molecule2'''
| |
| − | # Enjoy!
| |
| − | | |
| − | ===*nix systems===
| |
| − | ====Requirements====
| |
| − | * C compiler
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| − | * Python 2.4+ with distutils
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| − | * Numpy
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| − | ** for User-compiled PyMOL: <source lang="python">python setup.py install</source>
| |
| − | ** for the precompiled version of PyMOL <source lang="python">python setup.py install --prefix "" --root /DIR_TO/pymol/ext/</source>
| |
| − | | |
| − | ====Directions====
| |
| − | # uncompress the distribution file '''cealign-VERSION.tgz'''
| |
| − | # cd cealign-VERSION
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| − | # sudo python setup.py install # if you installed by PyMOL by hand
| |
| − | ## python setup.py install --prefix "" --root /DIR/TO/pymol/ext/ # if you are using the precompiled binary download
| |
| − | # insert "run DIR_TO_CEALIGN/cealign.py" and "run DIR_TO_CEALIGN/qkabsch.py" into your '''.pymolrc''' file, or just run the two Python scripts by hand.
| |
| − | # load some molecules
| |
| − | # run, '''cealign molecule1, molecule2'''
| |
| − | # enjoy
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| − | | |
| − | =====Pre-compiled Hackish Install=====
| |
| − | For those people that prefer to use the pre-compiled version of PyMOL, here are the basics for your install. '''This is a poor method of installing Cealign. I suggest users compile and install their own PyMOL.''' The final goal is to get
| |
| − | # '''ccealign.so''' module into '''PYMOL/ext/lib/python2.4/site-packages'''
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| − | # numpy installed (get the numpy directory into (or linked into) '''PYMOL/ext/lib/python2.4/site-packages'''
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| − | # and be able to run cealign.py and qkabsch.py from PyMOL.
| |
| − | If you can do the above three steps, '''cealign''' should run from the pre-compiled PyMOL.
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| − | | |
| − | In more detail, on a completely fictitious machine --- that is, I created the following commands from a fake machine and I don't expect a copy/paste of this to work '''anywhere''', but the commands should be helpful enough to those who need it:
| |
| − | <source lang="python">
| |
| − | # NOTES:
| |
| − | # This is fake code: don't copy/paste it.
| |
| − | #
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| − | # PYMOL='dir to precompiled PyMOL install'
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| − | # CEALIGN='dir where you will unpack cealign'
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| − | # replace lib with lib64 for x86-64
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| − | # install numpy
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| − | apt-get install numpy
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| − | | |
| − | # link numpy to PyMOL
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| − | ln -s /usr/local/lib/python2.4/site-packages/numpy PYMOL/ext/lib/python2.4/site-packages
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| − | | |
| − | # download and install Cealign
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| − | wget http://www.pymolwiki.org/images/e/ed/Cealign-0.6.tar.bz2
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| − | tar -jxvf Cealign-0.6.tar.bz2
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| − | cd cealign-0.6
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| − | sudo python setup.py build
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| − | cp build/lib-XYZ-linux/ccealign.so PYMOL/ext/lib/python2.4/site-packages
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| − | | |
| − | # run pymol and try it out
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| − | pymol
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| − | run CEALIGN/cealign.py
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| − | run CEALIGN/qkabsch.py
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| − | fetch 1cew 1mol, async=0
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| − | cealign 1c, 1m
| |
| − | </source>
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| − | | |
| − | == The Code ==
| |
| − | Please unpack and read the documentation. All comments/questions should be directed to Jason Vertrees (javertre _at_ utmb ...dot... edu).
| |
| − | | |
| − | '''LATEST IS v0.8-RBS'''. (Dedicated to Bryan Sutton for allowing me to use his computer for testing.)
| |
| − | | |
| − | === Version 0.8-RBS ===
| |
| − | * BZ2 File [[Media:Cealign-0.8-RBS.tar.bz2|CE Align v0.8-RBS]]
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| − | * ZIP File [[Media:Cealign-0.8-RBS.zip|CE Align v0.8-RBS]]
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| − | | |
| − | == Coming Soon ==
| |
| − | * Windows binary
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| − | * Linux Binaries (32bit, x86-64)
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| − | * Better instructions for precompiled distributions
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| − | * Optimization
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| − | | |
| − | == Updates ==
| |
| − | | |
| − | === 2007-04-14 ===
| |
| − | v0.8-RBS source updated. Found the bug that had been plaguing 32-bit machines. This should be the last release for a little while.
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| − | | |
| − | ===2007-03-27===
| |
| − | v0.6 source code updated. The '''important''' things about this release are:
| |
| − | * a correction in the scoring algorithm (with improvements up to, and over 2Ang in RMSD)!
| |
| − | * cleaned up some memory issues
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| − | * provided the simple '''alignto''' command
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| − | * added (poor) installation notes for those people with a pre-compiled version.
| |
| − | | |
| − | ===2007-03-07===
| |
| − | This change was too small to make a whole new release. I just added a small script to do multiple structure alignments. Skip to the [[Cealign#Multiple_Structure_Alignments|Multiple Structure Alignment Section]] on this page.
| |
| − | | |
| − | Also, I provide the option of aligning based solely upon RMSD or upon the better CE-Score. See the '''References''' for information on the '''CE Score'''.
| |
| − | | |
| − | == Troubleshooting ==
| |
| − | | |
| − | Post your problems/solutions here.
| |
| − | | |
| − | === Unicode Issues in Python/Numpy ===
| |
| − | '''Problem''': Running/Installing cealign gives
| |
| − | <source lang="python">
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| − | Traceback (most recent call last):
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| − | File "/home/byron/software/pymol_1.00b17/pymol/modules/pymol/parser.py",
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| − | line 308, in parse
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| − | File "/home/byron/software/pymol_1.00b17/pymol/modules/pymol/parsing.py",
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| − | line 410, in run_file
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| − | File "qkabsch.py", line 86, in ?
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| − | import numpy
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| − | File "/usr/lib/python2.4/site-packages/numpy/__init__.py", line 36, in ?
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| − | import core
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| − | File "/usr/lib/python2.4/site-packages/numpy/core/__init__.py", line 5, in ?
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| − | import multiarray
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| − | ImportError: /home/byron/software/pymol/ext/lib/python2.4/site-packages/numpy/core/multiarray.so:
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| − | undefined symbol: _PyUnicodeUCS4_IsWhitespace
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| − | </source>
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| − | where the important line is
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| − | <source lang="python">
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| − | undefined symbol: _PyUnicodeUCS4_IsWhitespace
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| − | </source>
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| − | | |
| − | This problem indicates that your Numpy Unicode is using a different byte-size for unicode characters than is the Python distribution your PyMOL is running from. For example, this can happen if you use the pre-built PyMOL and some other pre-built Numpy package.
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| − | | |
| − | | |
| − | | |
| − | '''Solution''': Hand-install Numpy.
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| − | | |
| − | | |
| − | === LinAlg Module Not Found ===
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| − | '''Problem''': Running CE Align gives the following error message:
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| − | <source lang="python">
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| − | run qkabsch.py
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| − | Traceback (most recent call last):
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| − | File "/usr/lib/python2.4/site-packages/pymol/parser.py", line 285, in parse
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| − | parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names)
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| − | File "/usr/lib/python2.4/site-packages/pymol/parsing.py", line 407, in run_file
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| − | execfile(file,global_ns,local_ns)
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| − | File "qkabsch.py", line 86, in ?
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| − | import numpy
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| − | File "/usr/lib/python2.4/site-packages/numpy/__init__.py", line 40, in ?
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| − | import linalg
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| − | ImportError: No module named linalg
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| − | </source>
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| − | | |
| − | | |
| − | | |
| − | '''Solution''': You do not have the linear algebra module installed (or Python can't find it) on your machine. One workaround is to install [http://www.scipy.org/ Scientific Python]. (on debian/ubuntu this can be done by: sudo apt-get install python-scipy) Another is to reinstall the Numpy package from source, ensuring that you have the necessary requirements for the linear algebra module (linpack, lapack, fft, etc.).
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| − | | |
| − | === CCEAlign & NumPy Modules Not Found ===
| |
| − | '''Problem''': Running CE Align gives the following error message:
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| − | <source lang="python">
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| − | PyMOL>run cealign.py
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| − | Traceback (most recent call last):
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| − | File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parser.py", line 297, in parse
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| − | File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 408, in run_file
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| − | File "/usr/local/pymol/scripts/cealign-0.1/cealign.py", line 59, in ?
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| − | from ccealign import ccealign
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| − | ImportError: No module named ccealign
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| − | run qkabsch.py
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| − | Traceback (most recent call last):
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| − | File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parser.py", line 297, in parse
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| − | File "/home/local/warren/MacPyMOL060530/build/Deployment/MacPyMOL.app/pymol/modules/pymol/parsing.py", line 408, in run_file
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| − | File "qkabsch.py", line 86, in ?
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| − | import numpy
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| − | ImportError: No module named numpy
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| − | </source>
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| − | | |
| − | | |
| − | | |
| − | '''Solution''': This problem occurs under [http://www.apple.com/macosx Apple Mac OS X] if (a) the Apple's python executable on your machine (/usr/bin/python, currently version 2.3.5) is superseded by [http://fink.sourceforge.net/ Fink]'s python executable (/sw/bin/python, currently version 2.5) and (b) you are using [http://delsci.com/rel/099/#MacOSX precompiled versions of PyMOL] (MacPyMOL, PyMOLX11Hybrid or PyMOL for Mac OS X/X11). These executables ignore Fink's python and instead use Apple's - so, in order to run CE Align, one must install NumPy (as well as CE Align itself) using Apple's python. To do so, first download the [http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=175103 Numpy source code archive] (currently version 1.0.1), unpack it, change directory to numpy-1.0.1 and specify the full path to Apple's python executable during installation: <tt>sudo /usr/bin/python setup.py install | tee install.log</tt>. Then, donwload the [http://www.pymolwiki.org/index.php/Cealign#The_Code CE Align source code archive] (currently version 0.2), unpack it, change directory to cealign-0.2 and finally install CE Align as follows: <tt>sudo /usr/bin/python setup.py install | tee install.log</tt>.
| |
| − | [[User:Lucajovine|Luca Jovine]] 05:11, 25 January 2007 (CST).
| |
| − | | |
| − | == References ==
| |
| − | Text taken from PubMed and formatted for the wiki. The first reference is the most important for this code.
| |
| − | | |
| − | # Shindyalov IN, Bourne PE. '''Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.''' ''Protein Eng.'' 1998 Sep;11(9):739-47. PMID: 9796821 [PubMed - indexed for MEDLINE]
| |
| − | # Jia Y, Dewey TG, Shindyalov IN, Bourne PE. '''A new scoring function and associated statistical significance for structure alignment by CE.''' ''J Comput Biol.'' 2004;11(5):787-99. PMID: 15700402 [PubMed - indexed for MEDLINE]
| |
| − | # Pekurovsky D, Shindyalov IN, Bourne PE. '''A case study of high-throughput biological data processing on parallel platforms.''' ''Bioinformatics.'' 2004 Aug 12;20(12):1940-7. Epub 2004 Mar 25. PMID: 15044237 [PubMed - indexed for MEDLINE]
| |
| − | # Shindyalov IN, Bourne PE. '''An alternative view of protein fold space.''' ''Proteins.'' 2000 Feb 15;38(3):247-60. PMID: 10713986 [PubMed - indexed for MEDLINE]
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| − | | |
| − | == License ==
| |
| − | The CEAlign and all its subprograms that I wrote, are released under the open source Free BSD License (BSDL).
| |
| − | | |
| − | | |
| − | [[Category:Script_Library]]
| |
| − | [[Category:Structure_Alignment|Cealign]] | |
