Dear Benn
Good Day !!!!!!!!!!!!!
I had run MODELLER to produced model 1-100.pdb (100 models) of same acid sequence but different energy values. Now, i want to calculate the RMSD values for the models. I know that SUPERPOSE will do for me. But i couldnot correlate and implement the results.
Say in VMD 1.8.4 in the RMSD calculator option, if Average is selected, VMD first computes the average x, y, z coordinates of the selected atoms in each molecule, then computes the RMS distance of each molecule from that average structure.
By the same manner, my first model is model1.pdb and now is superpose my model2.pdb and calculate an averaged RMSD. And on the next step i have to superpose my model3.pdb to the averaged structure and calculate new averaged RMSD and so on.
model1.pdb | superposition | model2.pdb | now two structures are merged/superposed | calculate the averaged RMSD for the merged/superposed structure | now superpose model3.pdb to the existing superposed structure (model1.pdb+model2.pdb) | now totally 3 structures are superposed | CALCULATE AVERAGED RMSD FOR PRESENT SUPERPOSED STRUCTURE (MODEL1+MODEL2+MODEL3) and so on
Could you please help me in carrying out the problem. can you help me in knowing how the script file looks.
WIth regards robert
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Robert Selwyne wrote: > I had run MODELLER to produced model 1-100.pdb (100 models) of same acid > sequence but different energy values. Now, i want to calculate the RMSD > values for the models. I know that SUPERPOSE will do for me. But i > couldnot correlate and implement the results.
You can align multiple structures with alignment.compare_structures() (see http://salilab.org/modeller/manual/node193.html), alignment.malign3d() (see http://salilab.org/modeller/manual/node195.html) or alignment.salign().
> Say in VMD 1.8.4 in the RMSD calculator option, if *Average* is > selected, VMD first computes the average x, y, z coordinates of the > selected atoms in each molecule, then computes the RMS distance of each > molecule from that average structure.
This is essentially the same algorithm used by alignment.malign3d(). See the manual linked above.
There is an example in examples/commands/malign3d.py. If you are using automodel to build your models, you can ask it to automatically align the generated models and calculate many properties, including the RMS, by setting final_malign3d to True. See examples/automodel/model-fast.py for an example.
Ben Webb, Modeller Caretaker
I have another question. How could I output the *Average* structure generated in the MALIGN3D procedure? e.g, I have a NMR structure with 30 models, and I want to get its average structure.
On Thursday 01 June 2006 00:46, Modeller Caretaker wrote: > Robert Selwyne wrote: > > I had run MODELLER to produced model 1-100.pdb (100 models) of same acid > > sequence but different energy values. Now, i want to calculate the RMSD > > values for the models. I know that SUPERPOSE will do for me. But i > > couldnot correlate and implement the results. > > You can align multiple structures with alignment.compare_structures() > (see http://salilab.org/modeller/manual/node193.html), > alignment.malign3d() (see > http://salilab.org/modeller/manual/node195.html) or alignment.salign(). > > > Say in VMD 1.8.4 in the RMSD calculator option, if *Average* is > > selected, VMD first computes the average x, y, z coordinates of the > > selected atoms in each molecule, then computes the RMS distance of each > > molecule from that average structure. > > This is essentially the same algorithm used by alignment.malign3d(). See > the manual linked above. > > There is an example in examples/commands/malign3d.py. If you are using > automodel to build your models, you can ask it to automatically align > the generated models and calculate many properties, including the RMS, > by setting final_malign3d to True. See examples/automodel/model-fast.py > for an example. > > Ben Webb, Modeller Caretaker
Yun He wrote: > I have another question. How could I output the *Average* structure generated > in the MALIGN3D procedure? e.g, I have a NMR structure with 30 models, and I > want to get its average structure.
Use transfer_xyz after malign3d, with the cluster_cut option. This allows you to take the average of all structures, or the average of the largest cluster. See http://salilab.org/modeller/manual/node130.html
automodel will do this automatically for you, producing a 'cluster.ini' average structure and a 'cluster.opt', which is additionally optimized by conjugate gradients, if you call automodel.cluster() after automodel.make(). See http://salilab.org/modeller/manual/node54.html
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Robert Selwyne -
Yun He