Re: [modeller_usage] Error with the Mutate script

Dear Ben,

I double checked and added again. Getting the same error.

#molecular dynamics
    def refine(atmsel):
            # at T=1000, max_atom_shift for 4fs is cca 0.15 A.
            md = molecular_dynamics(cap_atom_shift=0.39, md_time_step=4.0,
                                                md_return='FINAL')
                init_vel = True
                    for (its, equil, temps) in ((200, 20, (150.0, 250.0, 400.0, 700.0, 1000.0)),
                                                            (200, 600,

              (1000.0, 800.0, 600.0, 500.0, 400.0, 300.0))):
                                for temp in temps:
                                            md.optimize(atmsel, init_velocities=init_vel, temperature=temp,

Regards

Arjun

On Tue, May 7, 2013 at 9:04 PM, Modeller Caretaker <" target="_blank">> wrote:

On 5/7/13 2:19 AM, Arjun Ray wrote:

I am trying to mutate a residue THR61. Using the script provided on the website, I am getting following error:

rayarjun$ python /usr/bin/mutate.py 1AV1.pdb 61 THR A > 1AV1.log
File "/usr/bin/mutate.py", line 36
def refine(atmsel):
^
IndentationError: unindent does not match any outer indentation level

This is a Python syntax error. Python is very sensitive to indentation. The original script at http://salilab.org/modeller/wiki/Mutate%20model is correctly formatted. Are you sure you copied it exactly from the website without changing the indentation?

Ben Webb, Modeller Caretaker
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Arjun Ray
Department of Theoretical Physics
School of Engineering Sciences
Royal Institute of Technology (KTH)
AlbaNova University Center
SE-106 91 Stockholm
Sweden

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