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Re: [modeller_usage] modeller_usage Digest, Vol 7, Issue 21



Mohan,

The model with the lower DOPE score is better. You should also
evaluate the _template_ with the DOPE score -- you can find a script
to do this in examples/commands/assess_dope.py. This will give you an
idea of how the model compares with your template.

Vadim

On Tue, Apr 8, 2008 at 12:36 PM,  <> wrote:
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>  Today's Topics:
>
>    1. Help <Traceback> ()
>    2. Regarding DOPE model assessment values (Mohan)
>       ()
>    3. Trouble running superpose on subsets of multichain        pdbs
>       (Jake Gunn-Glanville)
>
>
>  ----------------------------------------------------------------------
>
>  Message: 1
>  Date: Tue, 08 Apr 2008 17:45:57 +0300
>  From: 
>  Subject: [modeller_usage] Help <Traceback>
>  To: 
>  Message-ID: <>
>  Content-Type: text/plain;       charset=ISO-8859-7
>
>  Hi,
>  Unfortunately, after rpm modeller and after running it as following, I received
>  this message:
>
>  [root@195-251-18-90 modeller]# mod9v3
>  /home/georgios/modeller/scripts_of_modeller/script_1.top
>  Traceback (most recent call last):
>   File "<string>", line 1, in ?
>   File "/usr/lib/modeller9v3/modlib/modeller/top_interpreter/__init__.py", line
>  36, in run
>     self._runlines(self.lines)
>   File "/usr/lib/modeller9v3/modlib/modeller/top_interpreter/__init__.py", line
>  150, in _runlines
>     self._set_top_vars(vars)
>   File "/usr/lib/modeller9v3/modlib/modeller/top_interpreter/__init__.py", line
>  281, in _set_top_vars
>     raise IndexError("No '=' found in variable assignment")
>  IndexError: No '=' found in variable assignment
>
>  I have also tried to run modeller from python without success. The message I
>  recieved is the following:
>
>  [root@195-251-18-90 modeller]# python
>  Python 2.3.4 (#1, Mar 14 2006, 11:40:38)
>  [GCC 3.4.4 20050721 (Red Hat 3.4.4-2)] on linux2
>  Type "help", "copyright", "credits" or "license" for more information.
>  >>> mod9v3 /home/maria/modeller/scripts_of_modeller/script_1.top
>  Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>  NameError: name 'mod9v3' is not defined
>  >>>
>  Does anybody know what is wrong here?
>  With best regards, Maria.
>
>
>  ------------------------------
>
>  Message: 2
>  Date: 08 Apr 2008 16:05:51 +0100
>  From: 
>  Subject: [modeller_usage] Regarding DOPE model assessment values
>         (Mohan)
>  To: 
>  Message-ID: <>
>  Content-Type: text/plain; format=flowed; charset=ISO-8859-1
>
>
>
>  Dear Members,
>                                I have a query regarding the DOPE score for
>  the models.It is mentioned in the manual that models with lowest DOPE score
>  value are reliable. I am having two models right now with values -7000 and
>  -6000 respectively. I would like to know which one is the best among these
>  two based on the values.
>
>
>  Thanking You,
>
>  Mohan.
>
>
>
>
>  ------------------------------
>
>  Message: 3
>  Date: Tue, 8 Apr 2008 09:36:20 -0700
>  From: "Jake Gunn-Glanville" <>
>  Subject: [modeller_usage] Trouble running superpose on subsets of
>         multichain      pdbs
>  To: 
>  Message-ID:
>         <>
>  Content-Type: text/plain; charset="iso-8859-1"
>
>  Dear Modelling Community,
>
>  I have two pdb structures I am interested in superposing, using an alignment
>  I have created outside of modeller. The alignment is in pir format, and only
>  represents a single chain from each PDB (each PDB has multiple chains in
>  this case). Ideally, I would like to have the superposition be performed by
>  only considering a subset of the aligned residues that I define (the most
>  conserved positions).
>
>  I have already looked through the superpose.py example, converted my
>  alignment into pir format, and familiarized myself with the modeller
>  'selection' object. Unfortunately, I am running into problems when I attempt
>  to run the superposition. The pir alignment I am using is below:
>
>  >P1;1ck0
>  structureX:1ck0:1:H:216:H:Ab1:Human:2.0:0.10
>  QVQLQESGGGLVQPRGSLKLSCAASGFTFNTDAMNWVRQAPGKGLEWVARIRSKGFNFATYYADSVRDRFTISRD
>  DSQSMLYLQMNNLKTEDTGIYYCVRGRDGEAMDYWGQGTTLTVSSAKTTPPSVYPLAPM--------VTLGCLVK
>  GYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVN
>  *
>  >P1;1e4w
>  structureX:1e4w:1:H:211:H:Ab2:Human:2.0:0.10
>  QVQLQQPGAELVKPGASVKLSCKASGFTFTNYWMHWVKQRPGQGLEWIGEILPS--NGRTNYNEKFKTKATLTVD
>  KSSNTAYMQLSSLTSEDSAVYYCARSPS----DYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVK
>  GYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP
>  *
>
>  When I attempt to just swap out these pdbs and this alignment with the ones
>  in the example superpose.py, it returns an error, complaining that my
>  submitted sequence length does not match the pdb sequence length.
>
>  -bash-3.00$ mod9v3 superpose.py
>  Traceback (most recent call last):
>   File "superpose.py", line 17, in ?
>     r = atmsel2.superpose(mdl2, aln)
>   File "/usr/lib/modeller9v3/modlib/modeller/selection.py", line 476, in
>  superpose
>     fit, refine_local, rms_cutoff)
>  _modeller.ModellerError: chk_aln_340E> Number of residues in model (
>  427) does not match that in alignment (     211).
>
>
>  What am I doing wrong? The superpose.py I used is shown below.
>
>  # Example for: selection.superpose()
>
>  # This will use a given alignment to superpose Calpha atoms of
>  # one structure (2ctx) on the other (1fas).
>
>  from modeller import *
>
>  env = environ()
>  env.io.atom_files_directory = '/datasets/pdb/'
>
>  mdl  = model(env, file='1ck0')
>  mdl2 = model(env, file='1e4w')
>  aln = alignment(env, file='test.ali', align_codes=('1ck0', '1e4w'))
>
>  atmsel = selection(mdl).only_atom_types('CA')
>  r = atmsel.superpose(mdl2, aln)
>
>  # We can now use the calculated RMS, DRMS, etc. from the returned 'r'
>  object:
>  rms = r.rms
>  drms = r.drms
>  print "%d equivalent positions" % r.num_equiv_pos
>
>  mdl2.write(file='1e4w.fit')
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>  End of modeller_usage Digest, Vol 7, Issue 21
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