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Modeller 4 help!



Modeller users:

As a neophyte, both to homology modeling and to the program Modeller-4,
I am somewhat confused by the protocol to follow in order to generate a
model of my target enzyme.  I would be very grateful if the Modeller
user community could help get me going!

I have the sequence of my target, and five .pdb files of enzymes that
belong to the same family, and share between 30 - 50% sequence
similarity to the target.  I want to get a 'good' model of the target -
CPU time is not a problem, I would prefer to be thorough and get better
results.  

Can anybody suggest the procedure I should follow, from the beginning!  

What file do I begin with? Do I write this myself? What is it called?
How do I obtain an alignment file? MALIGN-3D? then CHECK_ALIGNMENT?
Which script files should I run?   mod model-default?
How do I account for the error noted in the newsgroup archives? 

Any suggestions appreciated!   

Similarly, if anyone has modified the basic script files to good effect,
I would appreciate a copy!

Thanks in advance,

Nick


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Nick Glover
Department of Chemistry
Simon Fraser University
8888 University Drive
Burnaby, BC
V5A 1S6
Canada