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:
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> 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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