David Frederiksen rmh at
Fri Feb 23 11:33:35 EST 1996

Kiyoshi Gotow wrote:
> When you see the argument window, the program "protml" is already running.
> The first word "protml" is unnecessary.  In addition to the input file
> format command "-I", you need to specify the model of analysis and other
> parameters that you want to use in the maximum likelihood method.  The file
> "PROTML.EXA" in the package may give you some idea of the model, search
> strategy or mode, and others given by ProtML 2.2.
> I hope this helps.
> Kiyoshi Gotow, Ph.D.
> Department of Human Life and Culture
> Junior College, Seitoku University
> gotow at

  Hello Kiyoshi,

  Thank you for your prompt reply.  I have tried what you suggested and the 
error message did clear up but I still believe I am doing something wrong.  
The output window does not display any of the results.  I change the command 
line to "-I-j-e-D surfaceprotein".  Perhaps I have too many parameters 
(switches) this time. I also tried modifying my original commands to "-I-j 
surfaceprotein" and still not results.  I looked at the FORMAT file that came 
with the package and the README file.  I could not view the .EXA file for some 
reason.  Perhaps I do not have an appropriate text editor.  Is there any 
documentation that has more detailed instructions about it's use?  Or perhaps 
you have futher suggestions.

  Some other commands I have tried:
      -I-j-e-i surfaceprotein
      -I-j-e-w surfaceprotein
      -I-j-i sufaceprotein
      -I-j-w surfaceprotein

Thank You For Your Time
David Frederiksen

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