[modeller_usage] Converting (old) top script to (new) python ones

[Eric Hajjar <>]

Hi , i've been using Modeller old versions with the old formet --> TOP.

The new "polished - python" interface looks really promising , but i'm 
spending now some time to see how to make things work !
I went throught all tutorials , and that is OK ,
but in my present case i want to add DISULFIDE RESTRAINTS  and i want to 
change the default "coordinate-output-names"
so if i understand right i have to NOT use the "automodel" class anymore...

Here starts the trouble !

Also: Before i was doing :
SUBROUTINE ROUTINE = 'special_patches'
PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '27' '50'
RETURN
END_SUBROUTINE

now , according to the manual :
"mdl.patch_ss_templates(aln)                                                                                                                                   

# Create the stereochemical restraints
mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False) "


If i follow those examples in the  manual  and try to read my alignement 
to write the correponding model-with patches constraints. i get a 
completely unfolded, linear protein as a result !

Here's my input :

seq="Criquet"  # my sequence
align="Criquet-1pce-modifiedbyhand.ali"   # my alignement
#align="Criquet-1pce.ali"
struct="1pceA"
#struct2="3ovo"
                                                                                                                                            

                                                                                                                                            

# Read the sequence, calculate its topology, and coordinates:
aln = alignment(env, file=align, align_codes=(struct))
# Superpose the two template structures without changing the alignment.
# This is for TRANSFER_XYZ to work properly. It relies on not reading
# the atom files again before TRANSFER_XYZ.
aln.malign3d(fit=False)
# This is for TRANSFER_XYZ to work properly.
# Restore the alignment, and add in the model sequence, 1fas:
aln.append(file=align, align_codes=(struct, seq))
mdl = model(env)
mdl.generate_topology(aln, sequence='Criquet')
mdl.transfer_xyz(aln)
mdl.build(initialize_xyz=True, build_method='INTERNAL_COORDINATES')
                                                                                                                                            

mdl.write(file=align+'.noSS')
# Create the disulfide bonds using equivalent disulfide bonds in templates:
mdl.patch_ss_templates(aln)
                                                                                                                                            

# Create the stereochemical restraints
mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False)
# Calculate energy to test the disulfide restraints (bonds, angles, 
dihedrals):
mdl.energy()


Then i got confused:
why i'm not able to reproduce a "simple" top script : read an alignement 
--> build a model !
with the model() class



Thanks in advance for looking at this



--
-----------------------------
Eric Hajjar
Phd Student in Molecular Modeling
University of Bergen , Computational Biology Unit 
BCCS/UNIFOB, Bergen, NORWAY

tel:(+47)55584029
mob:(+47) 98023282