[modeller_usage] Question about Make_restraints

[Alejandra Leo <>]

Hi all,

I have a problem using Modeller and maybe someone could  give a hand.

I have my alignment (ecoli-FINAL.pir), my query sequence
(Nei1Ecoli_exp), and as structural template I have a trace of
C-alpha atoms (E_Coli_Test85) that is very important that do not move from their
initial positions. The only thing I want to do is to add the other atoms needed to
complete the backbone to my C-alpha trace.

I created this script for running modeller:

----------------------------------------------------
READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'

READ_ALIGNMENT FILE = 'ecoli-FINAL.pir', ALIGN_CODES = 'E_Coli_Test85'
MALIGN3D FIT = off
SET ADD_SEQUENCE = on
READ_ALIGNMENT FILE = 'ecoli-FINAL.pir', ALIGN_CODES = ALIGN_CODES 'Nei1Ecoli_exp'
CHECK_ALIGNMENT
GENERATE_TOPOLOGY SEQUENCE = 'Nei1Ecoli_exp'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ = off
WRITE_MODEL FILE = 'Nei1Ecoli-test.ini'

MAKE_RESTRAINTS RESTRAINT_TYPE = 'DISTANCE', DYNAMIC_SPHERE = on
MAKE_RESTRAINTS DISTANCE_RSR_MODEL = 5
WRITE_RESTRAINTS FILE = 'Nei1Ecoli.rsr'
READ_MODEL FILE = 'Nei1Ecoli-test.ini'

PICK_RESTRAINTS
#OPTIMIZE
ENERGY
WRITE_MODEL FILE = 'Nei1Ecoli-test_1.final'

--------------------------------------------------------------------------

And everything was fine until the make_restraints point. Nei1Ecoli.rsr
created file only contains a header line and the rest is empty. I
supposse that I am not using this command in the right way, but what I
want to do is to tell the program
that keep fix the C-alpha coordinates and add the rest, and make the
optimization (now in comments), without moving it. Or if it woult be
strictly necesary, to get a final structure with a RMS value as low
as possible, with respect to my starting C-alpha trace. Any ideas
about creating the restraints file and invoke it from the top script?

Thanks in advance, any help will be very appreciated!

Best,
Sandra