I am trying to model difference versions of a protein; each differing by one or two amino acids.
I am then looking at differences in electrostatics.
The effect size I am looking at is quite small and there is considerable difference simply from differences in modeller - I believe this is because it starts at a different amino acid. Between models with identical sequence the RMSD is ~0.2, which although small is abolishing any meaningful difference I could expect to see form the one or two amino acid change.
Therefore, I wonder if there is a way to ask modeller to start at the same point in these molecules? I tried a.rand_model = None, but that doesn't appear to be the correct option.
Does anyone know how I can achieve this?
Many thanks for your help.
-- D Mallon Clinical Research Fellow
e: dhm31@cam.ac.uk m: 07879 200800 t: 01223 336975
On 6/6/13 4:00 AM, Dermot Mallon wrote: > Between models with > identical sequence the RMSD is ~0.2
This is expected behavior. Modeller models are samples from the set of all models that satisfy the restraints.
> Therefore, I wonder if there is a way to ask modeller to start at the > same point in these molecules? I tried a.rand_model = None, but that > doesn't appear to be the correct option.
It sounds like what you're looking for is rand_method, not rand_model. But Modeller will still optimize to satisfy the restraints, which will move things around. You could just take the initial model (the *.ini file) which is a PDB file of the model before randomization and optimization. This won't change unless you change your alignment and/or template structures. But since it's unoptimized it could contain clashes.
Ben Webb, Modeller Caretaker
I am trying to model a mutation of a molecule whose .pdb file contains the asymmetric unit as well as definitions for its symmetry operations. I would like to determine the effects on the biological assembly a given mutation may have and would therefore like to include the space group symmetry in the model. I have looked through the online manual and have thus far been unable to produce such a model.
On 6/14/13 9:56 AM, David Johnson wrote: > I am trying to model a mutation of a molecule whose .pdb file contains > the asymmetric unit as well as definitions for its symmetry operations. > I would like to determine the effects on the biological assembly a given > mutation may have and would therefore like to include the space group > symmetry in the model. I have looked through the online manual and have > thus far been unable to produce such a model.
Modeller doesn't have any support for crystallographic symmetry. It doesn't read the symmetry operations from PDB files, and also has no support for periodic images or boundary conditions. The closest I think you can get in Modeller is to use the existing symmetry restraint (see http://salilab.org/modeller/9.12/manual/node28.html) and make a few copies of your asymmetric unit, but it'll be expensive because you'll have to model those copies as well.
Ben Webb, Modeller Caretaker
Hi.
The software Swiss PDB Viewer (SPDBviewer) has an option to generate copies of your asymmetric or biological unity in any space group you choose. Maybe it can help.
Regards,
Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br
________________________________ From: Modeller Caretaker modeller-care@salilab.org To: David Johnson da.johnson.a@gmail.com Cc: modeller_usage@salilab.org Sent: Friday, June 14, 2013 6:10 PM Subject: Re: [modeller_usage] Modelling Asymmetric Unit with Symmetry
On 6/14/13 9:56 AM, David Johnson wrote: > I am trying to model a mutation of a molecule whose .pdb file contains > the asymmetric unit as well as definitions for its symmetry operations. > I would like to determine the effects on the biological assembly a given > mutation may have and would therefore like to include the space group > symmetry in the model. I have looked through the online manual and have > thus far been unable to produce such a model.
Modeller doesn't have any support for crystallographic symmetry. It doesn't read the symmetry operations from PDB files, and also has no support for periodic images or boundary conditions. The closest I think you can get in Modeller is to use the existing symmetry restraint (see http://salilab.org/modeller/9.12/manual/node28.html) and make a few copies of your asymmetric unit, but it'll be expensive because you'll have to model those copies as well.
Ben Webb, Modeller Caretaker
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David Johnson -
Dermot Mallon -
flavio seixas -
Modeller Caretaker