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Alignment File Format
P1;5fd structureX:5fd1:1 : :106 : :ferredoxin:Azotobacter vinelandii: 1.90: 0. AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAI FSEDEVPEDMQEFIQLNAELA EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*
First line: Specifies the protein code after the >P1; line identifier.
Second line:
Field 1: A specification whether structure is available or not.
valid values: structureX, structureM, structure, sequence
Field 2: PDB Code
Field 3-6: identifiers for the first residue, chain id, last residue and its chain id.
Field 7: Protein Name
Field 8: Source of Protein
Field 9: Resolution of crystallographic analysis
Field 10: R-Factor
Residue Numbers and Chain Ids
Residue Numbers:
Any real number or one of the following
:
FIRST: means first residue number LAST: means last residue number END: Last Residue in PDB file @ will match any residue number and chain id @:@ first residue of first chain
Chain Ids:
Actual Chain ids or @: meaning any chain
Alignment File Format
Template format of second line
the template structures must have at least the first two fields specified
Eg:
- structure:pdb_file is equivalent to
- structure:pdb_file: : : : : : : :
Target Format of Second Line
the target sequence must have the first field filled in.
Script File
• MODELLER is a
– command-line only tool
– has no graphical user interface
– You must provide it with a script file
containing MODELLER commands in Python
– You can use the examples provided in
modeller
– OR learn python
– http://www.python.org/doc/2.3.5/tut/
Environ class
• contains information about the MODELLER
environment,
• default values for many functions
• Usually it is the first class to be used in a
MODELLER script, as it provides methods to
create the other main classes.
• You can assign the new environ object to the
Python variable 'env' with the following:
env = environ()
Log object
• The log object allows you to control the amount
of information output to the MODELLER log file.
log.verbose()
This instructs MODELLER to display all log
output.
log.minimal()
This instructs MODELLER to only display
important outputs, and errors.
Automodel() class
• Prepare to build one or more comparative models
• Input parameters:
- “env” : object of environ() class
- alnfile : file containing template sequence
alignment in PIR format
- knowns: template files in alignment
- sequence: sequence code in alignment file of
the target
Automodel eg.
a = automodel(env,
alnfile = 'TvLDH-4mdhA.ali', # alignment filename
knowns = '4mdhA', # codes of the templates
sequence = 'TvLDH') # code of the target
automodel.make()
- To build all models
- You should call this command after
creating an automodel object and
setting any desired parameters, to then
go ahead and build all models.
a.make()
SCRIPT FILES
• EASY WAY
UNDERSTAND AND MODIFY EXAMPLE
PROGRAMS WHERE NEEDED
Running Modeller
Run MODELLER itself by typing the following at
the command prompt:
> mod8v1 model-default.py
Model File:
A number of intermediary files are created as the
program proceeds
After about 30 seconds on a Pentium IV
workstation, the final 1fdx
model is written to file 1fdx.B99990001.pdb.
Understanding results
- To find out how good is the model, you have to inspect
the log file.
- Search for the following keywords for information
- Check_a : to find out about the alignment
- _W> : to check for warning messages
- _E> : to check for the error messages
- If everything is OK so far, the most important part of the
log file is the output of the model.energy() command for
each model. This is where the violations of restraints are
listed. When there are too many too violated restraints,
more optimization or a different alignment is needed.
LOG FILE – Template alignment
check_ali___> Checking pairwise structural superpositions.
Equivalent CA pairs with distance difference larger than 6. angstroms:
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST
337 1 2 332 324 I A 11. 95 2 3 90 96 K G 6. 96 2 3 91 97 N P 7. 97 2 3 92 98 A G 7. 98 2 3 93 99 A M 7. 99 2 3 94 100 K E 6. 337 2 3 324 329 A G 9.
END OF TABLE
check_ali___> Checking the sequence-structure alignment.
Search for check_ali in log file
Log file - Target Template
Alignment
runcmd______> alignment.check() check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./\4mdhA.pdb Dynamically allocated memory at amaxstructure [B,kB,MB]: 2645671 2583.663 2. openf5__224_> Open 11 OLD SEQUENTIAL ./\4mdhA.pdb check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
END OF TABLE check_a_344_> << END OF COMMAND
Alignment position template residue id 1 residue id 2 name1 name2 dist
