[modeller_usage] Fwd: Fwd: automodel.max_molpdf recommended values and usage format

[Andrew Voronkov <>]

Something was wrong with that script, I have taken model-outputs.py modified it and it worked fine.

Best regards,
Andrew

-------- Пересылаемое сообщение  --------
08.11.2011, 16:41, "Andrew Voronkov" <>:

Does it have name molpdf? I can't find DOPE or GA341 words in the log file.
I have also got an error while ranking the solutions.
Like this? But I have both DOPE and GA341, which of them is this?

>>  Summary of successfully produced models:

Filename                          molpdf
----------------------------------------
chimera.B99990001.pdb         1580.34619
chimera.B99990002.pdb         1593.52393
chimera.B99990003.pdb         1693.15637
chimera.B99990004.pdb         1743.10718
chimera.B99990005.pdb         1586.12122
chimera.B99990006.pdb         1652.49170
chimera.B99990007.pdb         1477.14709
chimera.B99990008.pdb         1681.59668
chimera.B99990009.pdb         1625.87500
chimera.B99990010.pdb         1632.77686
chimera.B99990011.pdb         1689.23584
chimera.B99990012.pdb         1557.99890
chimera.B99990013.pdb         1622.84631
chimera.B99990014.pdb         1805.83228
chimera.B99990015.pdb         1525.45911

Also I have got an error while trying to select best solutions based on DOPE score (script is below):

ok_models.sort(lambda a,b:cmp(a[key]), b[key]))
KeyError: 'DOPE score'

Here is the script, which was used:

from modeller import *
from modeller.automodel import *
import sys

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 = ['.']
# Read in HETATM records from template PDBs
env.io.hetatm = True

a = automodel(env,
              alnfile  = '2rf53mhj.pir', # alignment filename
              knowns   = ('3mhj', '2rf5'),     # codes of the templates
              sequence = 'chimera')               # code of the target
assess_methods=(assess.DOPE, assess.GA341) # assess each loop with DOPE
a.starting_model= 1                 # index of the first model
a.ending_model  = 15                 # index of the last model
                                    # (determines how many models to calculate)
# Thorough MD optimization:
a.md_level = refine.slow

a.make()                            # do the actual homology modeling

# Get a list of all successfully built models from a.outputs
ok_models = [x for x in a.outputs if x['failure'] is None]

# Rank the models by DOPE score
key = 'DOPE score'
if sys.version_info[:2] == (2,3):
    # Python 2.3's sort doesn't have a 'key' argument
    ok_models.sort(lambda a,b: cmp(a[key], b[key]))
else:
    ok_models.sort(key=lambda a: a[key])

# Get top model
m = ok_models[0]
print("Top model: %s (DOPE score %.3f)" % (m['name'], m[key]))

Best regards,
Andrew

07.11.2011, 19:51, "Modeller Caretaker" <>:

>  On 11/7/11 5:21 AM, Andrew Voronkov wrote:
>>   Dear Ben, very simple question . I have used DOPE assessment, but in
>>   which file can I find the assessment results for the models? It's not
>>   in resulted PDB, there is only objective function.Where can I find
>>   those DOPE and GA341 values?
>  In the log file. They are not put in the PDB file.
>
>          Ben Webb, Modeller Caretaker
>
>  --
>               http://www.salilab.org/modeller/
>  Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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