Dear Modeler mailing list,
I am a user of MODELLER 6v2 for Linux, and I am using this program to
model the mutations that I am making on CD1b. I am looking for new
interactions between amino acids that could be generated by these
mutations and for possible changes generated in loops. This is the
modeller that I am using:
INCLUDE
SET ATOM_FILES_DIRECTORY = '/home/moodyb/Miguel/37t/'
SET OUTPUT_CONTROL = 1 1 1 1 1
#SET PDB_EXT = '.pdb'
#SET MD_LEVEL = 'refine1'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 5
#SET DEVIATION = 4.0
SET KNOWNS = 'CD1b'
#SET HETATM_IO = off
#SET WATER_IO = off
#SET HYDROGEN_IO = off
#SET ALIGNMENT_FORMAT = 'PIR'
SET SEQUENCE = 'CD1b-37t'
SET ALNFILE = '37t.pir'
CALL ROUTINE = 'model'
Are these parameters the best way to get my objectives? I do not have much
experience in computer science, and I went through your manual and I did
not understand it at all. Please contact me with any advice and if it is
not convenient, could you tell me who might be able to help me?
Thank you very much.
Miguel Relloso.
----------------------oOO-(_)-OOo----------------
Miguel Relloso Ph.D.
Brigham & Women's Hospital
Harvard Medical School
Smith 514
1 Jimmy Fund Way
Boston, MA 02115
phone: 617.525.1027
fax: 617.525.1010