Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

Exon_68 Sali Lab Modeller4 Program at MUSC.

MUSC has licensed Modeller4:


Modeller4 Homology Modelling with spatial constraints.

The first thing you do is consult the on-line manual. Modeller
is typically run from scripts written in a special language
called TOP. There is no slick GUI for Modeller. Your best bet is to 

read the MANUAL FIRST!!!!. 

The second thing you do is try to run the examples from the manual.


To gain access here at MUSC you must modify your ".cshrc" file to 
include the following lines:


### begin modeller4 #######################################################
#
# Environment definitions for the main MODELLER version:
#
     # Root directory for the Protein DataBank (not essential, can be omitted):
     setenv PDB /disk2/pdb

     # MODELLER key (obtained from Andrej Sali at sali@rockvax.rockefeller.edu):
     setenv KEY MODELIRANJE

     # Root directory for installed MODELLER:
     setenv MODINSTALL /usr/common/bcr/modeller4

     # Set MODELLER environment variables and update the command path:
     if (-e $MODINSTALL/bin/setmodeller) source $MODINSTALL/bin/setmodeller
#
### end modeller4 #######################################################

When you've saved your modified ".cshrc" file you will need to type 

source .cshrc

or logout and login in again for the changes to take effect.

The Modeller program likes to see its template files in PDB format and
its model subject sequences AND the template sequences in a PIR format
with the gaps in place. You can also use the output of the CLUSTALW
program (one output option in the NBRF/PIR alignment option) to create
your initial alignments. See also the Modeller ALIGN and MALIGN programs.
NB the Modeller manual is rather emphatic that initial alignments often need 
to be tweaked for optimal use in homology modelling.

Here's an example alignment file (from the manual) which you might call
alignment.ali to go with the following TOP script.

------------------snip here---------------------------------------------------

>P1;5fd1
structureX:5fd1:   1 : : 106 : :ferredoxin:Azotobacter vinelandii: 1.90:0.192
AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA
EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*

>P1;1fdx
sequence:1fdx:   1 : :  54 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00
AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED*

-----------------snip here----------------------------------------------------

Here's an example script file (its from the manual) which you might name 
model-firsttry.top
------------snip here---------------------------------------------

# Homology modelling by the MODELLER TOP routine 'model'.

INCLUDE                             # Include the predefined TOP routines

SET ALNFILE  = 'alignment.ali'      # alignment filename
SET KNOWNS   = '5fd1'               # codes of the templates
SET SEQUENCE = '1fdx'               # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files
SET STARTING_MODEL= 1               # index of the first model
SET ENDING_MODEL  = 1               # index of the last model
                                    # (determines how many models to calculate)

CALL ROUTINE = 'model'              # do homology modelling

---------------------------snip here---------------------------------
  

Of course to use these example scripts you will need to get the 5df1 file from
RCSB. 

With all the files in place and your ".cshrc" file modified, typing

mod model-firsttry

ought to launch the program. Look into "model-firsttry.log" to see any errors.

Good Luck!

   
 

The BCR at the Medical University of South Carolina
URL: http://bcr.musc.edu/
Last modified: April 20, 2001- ESH

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