April 2008 - modeller_usage

Error when using dope_loopmodel
by Florian Odronitz 07 May '08

07 May '08

Hi, i generated a model using the model_single.py example. So this is without loop modeling. Now I would like to model loops only, using the example from the manual: from modeller import * from modeller.automodel import * class my_lm(dope_loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('535', '562')) env = environ() a = my_lm(env, alnfile='HsMhc1_best_no_loops_motor.ali', knowns='1DFK_motor', sequence='HsMhc1') a.starting_model = 1 a.ending_model = 1 a.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 5 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() Please note that I used the dope_loopmodel class instead of loopmodel as indicated in the manual. When I run the script, it exits with the following message: report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 1 68 111 445 496 671 602 791 874 924 1041 << end of ENERGY. iatmcls_286W> MODEL atom not classified: GLU:OXT GLU preppdf_458W> Both Lennard-Jones and statistical potential terms selected. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. check_inf__E> Atom 4293 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. Using dopehr_loopmodel gives the same error whereas the "old" loopmodel works. Here is the Atom record from the PDB file: ATOM 4293 N LEU 535 10.568 18.659 81.951 1.00103.06 1SG4294 The coordinates do not seem to be out of range. I also put a blank in the middle ("1.00 103.06") to avoid problems with the parser, but to no avail. Am I doing something wrong here or is this a bug? Any help on this is greatly appreciated. Florian

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Hang/crash on clustering
by James Irving 27 Apr '08

27 Apr '08

Hi all, I'm using Modeller 9v3 (Linux) and 9v1 (WindowsXP). I perform a rudimentary automodel with the script below. On both systems I get 200 output models, all of which appear to have an identical number of residues and atoms, however the script just hangs when it executes the cluster command. ---------------- # Homology modeling by the automodel class from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './' a = automodel(env, alnfile = 'sequences3.pir', knowns = ('prot1','prot2','prot3'), sequence = 'protx', assess_methods = (assess.GA341, assess.DOPE)) a.starting_model= 1 a.ending_model = 200 a.make() a.cluster() ----------------- I've then used the clustering script found at http://salilab.org/modeller/wiki/Cluster_PDBs with the 200 models, which uses transfer_xyz. This time the script ends with a segmentation fault (Linux) or closes unexpectedly (Windows XP). There are are no errors reported in the log file in either instance, it simply executes fine up to the point where clustering is requested and gets no further. As this hasn't been mentioned before I assume it's not a bug. Has anyone else had this problem and overcome it? Thanks! James

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Error message: attempting superposition based on a subset of positions
by Jake Gunn-Glanville 18 Apr '08

18 Apr '08

I have an input alignment, two structures, and a subset of residues I would like to use to perform a superposition. When I perform the superposition using all residues in the alignment I am successful. However, when I attempt to perform the superposition using a subset, I get error messages: The script: from modeller import * env = environ() log.very_verbose() env.io.atom_files_directory = '.' aln = alignment(env, file='reference.1dlf_L.pir', align_codes=('1ck0', '1dlf')) mdl1 = model(env, file='1ck0', model_segment=aln['1ck0'].range) mdl2 = model(env, file='1dlf', model_segment=aln['1dlf'].range) atmsel = selection(mdl1.residue_range('19', '23'), mdl1.residue_range('35', '39')) r = atmsel.superpose(mdl2, aln) mdl2.write(file='1dlf.subset.pdb') The alignment: >P1;1ck0 structureX:1ck0:FIRST:L:LAST:L:Ab:species:: DIQLTQSPS-SLAVSAGEKVTMNCKSSQNLLHSITR--KNYLAWYRQKPGQSPKLLIYW---ASTRGSGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYC---KQSYNL-YTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR * >P1;1dlf structureX:1dlf:FIRST:L:LAST:L:Ab:species:: DVVMTQ-TPLSLPVSLGNQASISCRSSQS---LVHSNGNTYLHWYLQKPGQSPKLLIYK---VSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFC---SQSTHVPFTFGSGTKLEIKR------------------------------------------------------------------------------------------------------- * The Error: Traceback (most recent call last): File "modelscript.1ck0.1dlf.py", line 10, in ? atmsel = selection(mdl1.residue_range('19', '23'), mdl1.residue_range('35', '39')) File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 71, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 198, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v3/modlib/modeller/util/modutil.py", line 19, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 56, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 19'

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superposition based on a subset of aligned residues
by Jake Gunn-Glanville 18 Apr '08

18 Apr '08

Hi modeller uage, Thanks again for your earlier comments and example code. Further along in the same project, I have a new question. I am attempting to superpose two structures given an input alignment, and I would like to restrict the superposition to only consider a subset of the aligned residues. For example, I might want the two structures superposed by only considering a few of the most conserved residues. I can probably figure out how to do this by combining selections, but since your last correspondence had such an elegant solution to my last problem, I thought I'd ask your advice on this one as well. Cheers, Jacob Glanville

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secondary structure restraints
by Marta Rossini 18 Apr '08

18 Apr '08

Hi all, my problem is the following: I have in my template an alpha helix of around 20 residues, and in my model I have to extend it by forcing the secondary structure (additional residues are not present in the template). The problem is that, both by introducing secondary structure restraints in the whole segment or only in the additional residues, I'm not able to obtain a straightened helix (the total number of alpha helix residues will be around 54), since Modeller introduces a strange bending in the helix (maybe because it is "too long"?). I would like simply to extend the starting helix in the same direction (that is, by keeping the starting helix axis up to the end). Is there a way (like another restraint to add) to avoid this "curvature" ? Thanks in advance _________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx

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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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