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.
On Tue, Apr 8, 2008 at 12:36 PM, firstname.lastname@example.org wrote: > Send modeller_usage mailing list submissions to > email@example.com > > 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 > firstname.lastname@example.org > > You can reach the person managing the list at > email@example.com > > 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> (firstname.lastname@example.org) > 2. Regarding DOPE model assessment values (Mohan) > (email@example.com) > 3. Trouble running superpose on subsets of multichain pdbs > (Jake Gunn-Glanville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 08 Apr 2008 17:45:57 +0300 > From: firstname.lastname@example.org > Subject: [modeller_usage] Help <Traceback> > To: email@example.com > Message-ID: firstname.lastname@example.org > 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: email@example.com > Subject: [modeller_usage] Regarding DOPE model assessment values > (Mohan) > To: firstname.lastname@example.org > Message-ID: Prayer.email@example.com > 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" firstname.lastname@example.org > Subject: [modeller_usage] Trouble running superpose on subsets of > multichain pdbs > To: email@example.com > Message-ID: > firstname.lastname@example.org > 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') >
Vadim Patsalo wrote: > 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.
There is very little value in comparing the model with the template, since by construction it should look similar. Plus, DOPE scores are not normalized, so you cannot compare them for different structures. One thing you can do is plot DOPE profiles for both template and model and compare them by eye, as this gives you a rough idea whether your alignment is correct. See the end of the basic tutorial on the Modeller website for an example.
Ben Webb, Modeller Caretaker