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