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, modeller_usage-request@salilab.org wrote: > Send modeller_usage mailing list submissions to > modeller_usage@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Help <Traceback> (matziast@med.uth.gr) > 2. Regarding DOPE model assessment values (Mohan) > (m.b.rajasekaran@reading.ac.uk) > 3. Trouble running superpose on subsets of multichain pdbs > (Jake Gunn-Glanville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 08 Apr 2008 17:45:57 +0300 > From: matziast@med.uth.gr > Subject: [modeller_usage] Help <Traceback> > To: modeller_usage@salilab.org > Message-ID: 20080408174557.4ghmelm3dssg0k00@webmail.uth.gr > 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: m.b.rajasekaran@reading.ac.uk > Subject: [modeller_usage] Regarding DOPE model assessment values > (Mohan) > To: modeller_usage@salilab.org > Message-ID: Prayer.1.0.18.0804081605510.17120@vimb4.rdg.ac.uk > 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" dr.jake@gmail.com > Subject: [modeller_usage] Trouble running superpose on subsets of > multichain pdbs > To: modeller_usage@salilab.org > Message-ID: > aee8e2e20804080936veb34e04le635bef6bc9dcc40@mail.gmail.com > 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') >