Hi
After having built my models, i have decided to assess them using the ga341 score. the script i am using is:
# Example for: model.assess_ga341()
env = environ()
# Read a model previously generated by Modeller's automodel class mdl = model(env, file='.59.pdb')
# Set template-model sequence identity. (Not needed in this case, since # this is written by Modeller into the .pdb file.) mdl.seq_id = 30.174
score = mdl.assess_ga341()
the ouput of this script for two different models is:
model1 % sequence identity : 30.174000 Sequence length : 531 Compactness : 0.270804 Native energy (pair) : -225.273799 Native energy (surface) : -13.946407 Native energy (combined) : -6.357012 Z score (pair) : -9.813731 Z score (surface) : -7.147611 Z score (combined) : -11.464915 GA341 score : 1.000000
model2 % sequence identity : 30.174000 Sequence length : 531 Compactness : 0.256617 Native energy (pair) : -268.422282 Native energy (surface) : -16.727187 Native energy (combined) : -7.618686 Z score (pair) : -9.969647 Z score (surface) : -7.755271 Z score (combined) : -12.156111 GA341 score : 1.000000
how do i interpret these outputs? should both scores be 1?
Jo
jo hanna wrote: > After having built my models, i have decided to assess them using the > ga341 score.
> the ouput of this script for two different models is: > > model1 > GA341 score : 1.000000 > > model2 > GA341 score : 1.000000 > > how do i interpret these outputs? should both scores be 1?
GA341 is not sufficiently sensitive to distinguish between two 'very good' models. Any good model will give a score very close to 1 (e.g. running GA341 on most PDB structures will give a 1.0 score). You should use it only to discard 'bad' models (e.g. those with score less than 0.6). DOPE may be more sensitive in your case.
Ben Webb, Modeller Caretaker
How can I get those ga341 and DOPE scores? I used to evaluate my models using only Procheck, Whatcheck and Verify3D (and of course modeller energy function).
Lucas
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Hi
Okay I have calculated the DOPE scores and I will use these. Just out of interest, is there are way of utilising the Z scores or compactness scores from GA341? From the example below I am assuming that the lower the Z score the better, would this be correct? Also when it comes to the compactness value is a higher or lower score better?
Many thanks Jo
model1 % sequence identity : 30.174000 Sequence length : 531 Compactness : 0.270804 Native energy (pair) : -225.273799 Native energy (surface) : -13.946407 Native energy (combined) : -6.357012 Z score (pair) : -9.813731 Z score (surface) : -7.147611 Z score (combined) : -11.464915 GA341 score : 1.000000
model2 % sequence identity : 30.174000 Sequence length : 531 Compactness : 0.256617 Native energy (pair) : -268.422282 Native energy (surface) : -16.727187 Native energy (combined) : -7.618686 Z score (pair) : -9.969647 Z score (surface) : -7.755271 Z score (combined) : -12.156111 GA341 score : 1.000000 On 2/21/06, Modeller Caretaker modeller-care@salilab.org wrote: > > jo hanna wrote: > > After having built my models, i have decided to assess them using the > > ga341 score. > > > the ouput of this script for two different models is: > > > > model1 > > GA341 score : 1.000000 > > > > model2 > > GA341 score : 1.000000 > > > > how do i interpret these outputs? should both scores be 1? > > GA341 is not sufficiently sensitive to distinguish between two 'very > good' models. Any good model will give a score very close to 1 (e.g. > running GA341 on most PDB structures will give a 1.0 score). You should > use it only to discard 'bad' models (e.g. those with score less than > 0.6). DOPE may be more sensitive in your case. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >
jo hanna wrote: > Okay I have calculated the DOPE scores and I will use these. Just out of > interest, is there are way of utilising the Z scores or compactness > scores from GA341? From the example below I am assuming that the lower > the Z score the better, would this be correct? Also when it comes to the > compactness value is a higher or lower score better?
Please refer to the GA341 paper (http://salilab.org/pdf/090_MeloProteinScience2002.pdf) and the MOULDER paper (http://salilab.org/pdf/123_JohnNAR2003.pdf) for more information.
Ben Webb, Modeller Caretaker
participants (3)
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jo hanna -
Lucas Bleicher -
Modeller Caretaker