- modeller_usage - salilab.org

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by eashwar annipindi 11 Apr '08

11 Apr '08

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Help <exec prefix>
by matziast＠med.uth.gr 09 Apr '08

09 Apr '08

Hi, I am grateful for your immediate and so important replies. Althouth I face serious problem. One month I am trying to start modeller. My scripts are named script_1.top/script_2.top... but it is impossible to start my diploma theses. I thought the probability my script is wrong and so I tried to run a script of the modeller's tutorial but the message I got is the following: [root@localhost test1]# mod9v3 TvLDH.ali Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback File "TvLDH.ali", line 1 >P1;TvLDH ^ SyntaxError: invalid syntax This message I always recieve but I don't understand what is wrong because the python is installed. On top of that I 've tried to run modeller from the python interpreter but the output message told me that mod9v3 is a script and not a command. Please help me. I don't know what to do. Thank you. With best regards, Maria.

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Trouble running superpose on subsets of multichain pdbs
by Jake Gunn-Glanville 08 Apr '08

08 Apr '08

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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Re: [modeller_usage] modeller_usage Digest, Vol 7, Issue 21
by Vadim Patsalo 08 Apr '08

08 Apr '08

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(a)salilab.org> wrote: > Send modeller_usage mailing list submissions to > modeller_usage(a)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(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)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(a)med.uth.gr) > 2. Regarding DOPE model assessment values (Mohan) > (m.b.rajasekaran(a)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(a)med.uth.gr > Subject: [modeller_usage] Help <Traceback> > To: modeller_usage(a)salilab.org > Message-ID: <20080408174557.4ghmelm3dssg0k00(a)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(a)reading.ac.uk > Subject: [modeller_usage] Regarding DOPE model assessment values > (Mohan) > To: modeller_usage(a)salilab.org > Message-ID: <Prayer.1.0.18.0804081605510.17120(a)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(a)gmail.com> > Subject: [modeller_usage] Trouble running superpose on subsets of > multichain pdbs > To: modeller_usage(a)salilab.org > Message-ID: > <aee8e2e20804080936veb34e04le635bef6bc9dcc40(a)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') >

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Help <Traceback>
by matziast＠med.uth.gr 08 Apr '08

08 Apr '08

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.

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modelling multiple sequences in one go
by navkaranj 08 Apr '08

08 Apr '08

hello I want to know that if I have, say about 10 target sequences that I want to model, each with a corresponding template structure, what is the sript that I will have to follow in order to model all of them in one run? Instead of 10 different scripts which make things cumbersome, I want to combine the result of all in one script in one run. please let me know if there is such a script and if there is none,could you assisst me to write one. thank you. navkaran

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Regarding DOPE model assessment values (Mohan)
by m.b.rajasekaran＠reading.ac.uk 08 Apr '08

08 Apr '08

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.

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running separate files from different folders
by navkaranj 07 Apr '08

07 Apr '08

i m tryin to model a number of proteins using modeller 9v3 . i would like to know if i can run all my files from diferent folders using 1 command. is it possible to run a common command in modeller , mentioning the directory/folder of proteins to be modelled , so as to model all proteins in their designated folders

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ALIGN_CODE
by barwellj＠aston.ac.uk 07 Apr '08

07 Apr '08

Hello modellers, I have just started using the programme and have already ran into some difficulty. I am trying to do a homology model .The error message I get suggests that my alignment file does not match my pdb file. Although, all my files are in the same directory as modeller and both written in the same case. I'm not sure why it is not working? Before running the programme I edited the PDB file using DEEPVIEW to remove the antagonist from the structure. Also I used GENEDOC to produce the alignment and saved it in a PIR format. Not sure if this has something to do with my problem? attached is my PDB file (called a.pdb), my alignment file (a.pir) and my script file (called script.py) and the log file. Any help would really be appreciated

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Re: [modeller_usage] modeller_usage Digest, Vol 7, Issue 19
by Vadim Patsalo 07 Apr '08

07 Apr '08

Hello, There seems to be a problem with your a.pir file. In particular, instead of structure:a.pdb:29::122::::: the file should read: structure:a.pdb:29:A:122:A:::: Note the difference, I am telling modeller to look for residue 29 of chain A in the pdb. otherwise, it looks like it looks for residue 29 of chain " ". Take a look at the manual to see how the PIR format works: http://www.salilab.org/modeller/manual/node421.html. Best, Vadim > Hello modellers, > > I have just started using the programme and have already ran into some > difficulty. I am trying to do a homology model .The error message I get > suggests that my alignment file does not match my pdb file. Although, all > my files are in the same directory as modeller and both written in the > same case. > > I'm not sure why it is not working? Before running the programme I edited > the PDB file using DEEPVIEW to remove the antagonist from the structure. > Also I used GENEDOC to produce the alignment and saved it in a PIR format. > Not sure if this has something to do with my problem? > > attached is my PDB file (called a.pdb), my alignment file (a.pir) and my > script file (called script.py) and the log file. > > Any help would really be appreciated

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