from one of our fellow MODELLERs... Can anyone help? B.. ---------- Forwarded Message ----------

Subject: modeller top files Date: Fri, 12 Jul 2002 12:17:13 +0100 From: "Rosh Karunaratne" <HIDDEN> To: bozidar@salilab.org

thanks for your help last week Ive been reading through the online modeller manual (version6) and am having trouble creating the 'right' top file for my ali file that I have created. Below are two of the examples i have tried (both using the modeller manual) but when I run procheck on the last *.B9999 file I get heavy violations and bad contatcs between atoms. All I am interested in is creating the 'best model' within least violations etc Is there a pre-prepared top file that you know of that will do this task?

Thanks for your help Rosh

INCLUDE #rho1

SET ALNFILE = 'name.ali' SET HETATM_IO = on SET KNOWNS = '1abc' SET SEQUENCE = '123456' SET ATOM_FILES_DIRECTORY = '/d/d120/u/fkaru01/' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET DO_LOOPS = '1' SET LOOP_STARTING_MODEL =1 SET LOOP_ENDING_MODEL= 25 SET LOOP_MD_LEVEL = 'refine_5' CALL ROUTINE = 'model'

or

SET ALNFILE = 'name.ali' SET KNOWNS = '1abc' SET SEQUENCE = '123456' SET ATOM_FILES_DIRECTORY = '/d/d120/u/fkaru01/' SET STARTING_MODEL = 2 SET ENDING_MODEL = 2

CALL ROUTINE = 'very_fast' CALL ROUTINE = 'model'

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