1) WHEN I RUN SUPEPOSE.py script i have got the follwing warninig how can i rectify

readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 8 Modeller will only read the first 80 characters of this line. readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 9 Modeller will only read the first 80 characters of this line. readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 10 Modeller will only read the first 80 characters of this line. readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 11 Modeller will only read the first 80 characters of this line. readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 12 Modeller will only read the first 80 characters of this line. readlinef__W> File: ../atom_files\1PY9_AO.pdb, Line: 13 No more warnings will be printed for truncated lines in this file.

2)WHEN I RUN model_evaluate.py i have got the follwing warninig how can i rectify

getf_______W> RTF restraint not found in the atoms list: residue type, indices: 5 529 atom names : C CA +N O atom indices : 4234 4226 0 4235

modeller_usage-request@salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage@salilab.org

To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request@salilab.org

You can reach the person managing the list at modeller_usage-owner@salilab.org

When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..."

Today's Topics:

1. loop optimization in the presence of a ligand (Thijs Beuming) 2. Re: loop optimization in the presence of a ligand (Modeller Caretaker) 3. Re: modeller_usage Digest, Vol 6, Issue 79 (vidhya sankar)

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

Message: 1 Date: Thu, 16 Aug 2007 16:21:11 -0400 From: "Thijs Beuming" Subject: [modeller_usage] loop optimization in the presence of a ligand To: modeller_usage@salilab.org Message-ID: 5C60D3FA-2EF9-44A4-A613-BA0C09614F12@med.cornell.edu Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed

Hi,

I am trying to optimize a loop in close proximity to a ligand. For some reason, the intial models have the ligand present, while the loop optimized models do not. Hence, there are major clashes between some of the calculated loops and the ligand. Is it possible to optimize loops in the presence of the ligand?

My input script:

# Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class

log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in

# directories for input atom files env.io.atom_files_directory = 'MODELLER'

class mymodel(loopmodel): def special_restraints(self, aln): rsr = self.restraints rsr.add(atom_ids=('CA:189', 'CA:372'), restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) rsr.add(atom_ids=('CA:189', 'CA:393'), restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) rsr.add(atom_ids=('CA:372', 'CA:393'), restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1))

def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['176'], self.residues ['185'])) def select_loop_atoms(self): return selection(self.residue_range('378:', '383:'))

a = mymodel(env, alnfile = 'MODELLER/alignment.pir', # alignment filename knowns = 'template', # codes of the templates sequence = 'target') # code of the target

a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model

a.loop.starting_model = 1 # First loop model a.loop.ending_model = 2 # Last loop model

a.make() # do the actual homology modeling

Thanks,

Thijs Beuming

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

Message: 2 Date: Thu, 16 Aug 2007 16:41:55 -0700 From: Modeller Caretaker Subject: Re: [modeller_usage] loop optimization in the presence of a ligand To: Thijs Beuming Cc: modeller_usage@salilab.org Message-ID: 46C4E0C3.5090904@salilab.org Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Thijs Beuming wrote: > I am trying to optimize a loop in close proximity to a ligand. For > some reason, the intial models have the ligand present, while the > loop optimized models do not. Hence, there are major clashes between > some of the calculated loops and the ligand. Is it possible to > optimize loops in the presence of the ligand?

It's hard to say for sure what your problem is without seeing all of your input files, but it looks like you haven't turned on env.io.hetatm, so I don't think you should be seeing ligands in either your regular models or your loop models.

You can see the restraints that loopmodel builds by looking at the loop_restraints() method in the modlib/modeller/automodel/loopmodel.py file. By default it builds stereochemical, phi/psi, and dihedral restraints, but not the ligand-protein restraints that automodel does. You could easily fix this to restrain ligands by overriding the special_restraints() method and calling automodel.nonstd_restraints() from there. Note however that the ligand-protein restraints may be too strong to allow your loop to explore much conformational space, so it may make sense to use weaker or fewer restraints here.

> def special_restraints(self, aln): > rsr = self.restraints > rsr.add(atom_ids=('CA:189', 'CA:372'), > restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) > rsr.add(atom_ids=('CA:189', 'CA:393'), > restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1)) > rsr.add(atom_ids=('CA:372', 'CA:393'), > restraint_parameters=(3, 1, 1, 27, 2, 2, 0, 10.0, 0.1))

Note that this way of specifying restraints is error prone and deprecated. You can see examples of the more robust method at http://salilab.org/modeller/9v2/manual/node209.html or http://salilab.org/modeller/tutorial/advanced.html

Ben Webb, Modeller Caretaker