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
wrote:
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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: Message-ID: <> 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'
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
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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: Message-ID: <> 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.
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 -- http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
can i compare th DOPE score of my mode with dope score of X-ray PDB.?if i can, what should be the DOPE SCORE difference between my model and X-ray PDB in order tobe my model is a reliable
model. could you please tell some difference in score value yhanks in advance
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i do not have proper PDB TEMPLATE for my 529 amino acid sequence.I have only the PDB of 53% sequence similiarity & identity. upon using this in superpose .py script i have got RMS OF 2.3337 and number of aligned equivalent positions 33 amog 115 residues will it be reliable value ?
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i did not get any log files when i run modeller9v1 in windowsXp .what shoul i do to get log files thank you? i am expecting your reply
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i have got a DOPE score of -41275.816406 is it reliable value ? .how can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE
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I have got a RMS and DRMS value of after super position 2.0482 and 1.5631 respectively.is it reliable value? .for 53.85% sequence identity i am expecting your reply
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I have got a RMS and DRMS value of after super position 2.0482 and 1.5631 respectively.is it reliable value? .for 53.85% sequence identity i am expecting your reply
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vidhya sankar wrote: > i have got a DOPE score of -41275.816406 is it reliable value ? .how > can i come to conclusions for my 3Dmodel .how can i analyse DOPE SCORE
The absolute value is essentially meaningless, so you can use it only to compare against other models of the same sequence, just like the Modeller molpdf score. See http://salilab.org/modeller/9v2/manual/node245.html
Ben Webb, Modeller Caretaker -- http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
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