October 2013 - modeller_usage

Fwd: [ModPipe-users] Installation Issues
by Amjad Farooq 18 Oct '13

18 Oct '13

Hi Ben, That worked. I was able to generate the "mod9.12" script inside /bin directory of modeller 9.12 under $MODPIPE/ext/mod/. However, when I run a test under /tests, I get the following error: > make ************************************************************************** cd unit && ../../int/runscript.sh python run-all-tests.py -v > /dev/null /bin/sh: ../../int/runscript.sh: No such file or directory make: *** [unit] Error 127 ************************************************************************** Where is this ../../int/runscript.sh script? The /int directory is empty! Also, when I run a demo under /demo, I get this error: ************************************************************************** Traceback (most recent call last): File "AddSeqMP.py", line 17, in <module> import modpipe.version ImportError: No module named modpipe.version ************************************************************************** Any thoughts on what I may be doing wrong? I have tried to follow installation instructions for MODPIPE as closely as possible: http://salilab.org/modpipe/doc/intro.html#getting-modpipe Thanks very much, Amjad ---------- Forwarded message ---------- From: Ben Webb <ben(a)salilab.org> Date: Fri, Oct 18, 2013 at 12:15 PM Subject: Re: [ModPipe-users] Installation Issues To: Help and discussion for users of ModPipe <modpipe-users(a)salilab.org> Cc: Amjad Farooq <amjad(a)farooqlab.net> On 10/17/13 7:50 PM, Amjad Farooq wrote: > How does one install MODELLER 9.12 inside ModPipe? I have MODELLER 9.12 > installed on a linux machine and it runs fine. But, I am having some > issues with installing MODELLER 9.12 inside ModPipe. > Download the Modeller .tar.gz installer, run the Install script, and tell it to install in $MODPIPE/ext/mod/. Once that's done, there should be a mod9.12 script in the bin subdirectory. Is there a way to tell ModPipe to read in automatically pre-installed > MODELLER 9.12 at another location > No, but you could probably make it work with some symlinks if you really don't want to have two copies of Modeller. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Fwd: Installation Issues
by Amjad Farooq 18 Oct '13

18 Oct '13

Dear Ben, How does one install MODELLER 9.12 inside ModPipe? I have MODELLER 9.12 installed on a linux machine and it runs fine. But, I am having some issues with installing MODELLER 9.12 inside ModPipe. According to the instructions, one should make changes to the $MODPIPE/ext/mod/bin/modXXX executable: http://salilab.org/modpipe/doc/install-ext.html#install-ext But, I do not see modXXX under the bin/ directory in MODELLER 9.12? The only scripts available under the bin/ in MODELLER 9.12 appear to be: mod9.12_i386-intel8 modpy.sh.in modslave.py Is there a way to tell ModPipe to read in automatically pre-installed MODELLER 9.12 at another location instead of installing it again under $MODPIPE/ext/mod/ on the same machine? Can you please help?! Thanks very much, Amjad *AMJAD FAROOQ PhD DIC | Associate Professor Dept of Biochemistry & Molecular Biology | Miller School of Medicine | University of Miami | Miami | FL 33136 Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL 33136 amjad(a)farooqlab.net | off 305-243-2429 | lab 305-243-9799 | fax 305-243-3955| www.farooqlab.net*

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extended conformations
by fantasticqhl 16 Oct '13

16 Oct '13

Dear all, I am trying to construct a model with two chains, the conformation of the template is extended helix, However, the conformations of the model I got were folded, the C-terminal is very close to the N-terminal. It is not extended which is what I want. How can I do to make sure that the conformation of the models are extended? All the best, Qinghua

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channel-like structure
by fantasticqhl 15 Oct '13

15 Oct '13

Hi all, I want to construct a model of channel-like hexamer based on a monomer peptide, is that possible with modeller? If yes, is there some similar tutorials, or could you please give me some suggestions? Thanks in advance! All the best, Qinghua

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constraints failed
by fantasticqhl 14 Oct '13

14 Oct '13

Dear all, I am trying to construct a model with four HIS binding to a copper. I set the distance constraints for ND1--CU as 2.0 angstrom, but the distances between ND1 and CU of the constructed models are around 2.5 angstrom, it seems that the constraints failed. Acctually, when I checked the model, I found that the distances could be around 2.0 angstrom if CU was just moved a little bit. rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['ND1:13:X'],at['CU:43:Y']), mean=2.00, stdev=0.05)) rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(at['ND1:14:X'],at['CU:43:Y']), mean=2.00, stdev=0.05)) Could someone tell me what kinds of reasons could result in restraints failure? Thanks very much! All the best, Qinghua

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problem in using mutate_model.py
by Anna Marabotti 10 Oct '13

10 Oct '13

Dear Modeller users, I created several mutants of my protein (which is a homodimeric protein) using the script mutate_model.py.and all has gone perfectly, but I have a problem in introducing a mutation. I want to introduce mutation in position 321 of both chains. So, I started introducing mutation in chain A using the command: mod9.11 - myprot 321 TYR A <mutate_model.py> myprotTYR321.log and all went OK. When I introduced the mutation in chain B starting from the mutant obtained in the previous step, using the command: mod9.11 - myprotTYR321 321 TYR B <mutate_model.py> myprotTYR321TYR321.log MODELLER gave me the following error message: OverflowError:check_inf__E> Atom 5347 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. The strange thing is that if I start introducing the mutation from chain B using the command: mod9.11 - myprot 321 TYR B <mutate_model.py> myprotTYR321-B.log MODELLER stops with the following error: OverflowError:check_inf__E> Atom 5345 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. I had a look at the original structure; atoms 5345 and 5347 are, respectively, atoms CB and O of the residue preceding the mutant one, and no apparent problems are present in the protein structure (no distortions, no aberrant structures - the residue is inserted into a beta sheet). But assuming that I have a problem on my structure, why the problem is not in the same atom when I start mutating from chain A or from chain B, considering that the procedure involves exactly the same residue? Thanks a lot for your help, best regards Anna -- ______________________________________________ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabotti(a)unisa.it Skype: annam1972 Web page: http://www.unisa.it/docenti/annamarabotti/index "Indifference is the eighth deadly sin" (don Andrea Gallo)

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Modelling with Side chain Restraints
by Lalith Kumar 09 Oct '13

09 Oct '13

Hi I want to build a complete structure for a protein that has partial crystal structure available but with out any deviations for the side chains of residues that are copied from template (crystal structure). Please let me know if there is any script available for restraining side chains of these residues. with kind regards, lalith

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Re: [modeller_usage] modeller_usage Digest, Vol 12, Issue 55
by Rajesh gazara 03 Oct '13

03 Oct '13

first u have to align your target with template using align2d.py when alignment will created >P1;1ze9A structureX:1ZE9.pdb: 1 :A:+16 :A:::-1.00:-1.00 DAEFRHDSGYEVHHQK* >P1;ABCD sequence:ABCD: : : : ::: 0.00: 0.00 DAEFRHDSGYEVHHQK* like this. then change it like below:- >P1;1ze9A structureX:1ZE9.pdb: 1 :A:+16 :A:::-1.00:-1.00 DAEFRHDSGYEVHHQK.* >P1;ABCD sequence:ABCD: : : : ::: 0.00: 0.00 DAEFRHDSGYEVHHQK.* and use model-ligand.py script to build model. gudluck On Wed, Oct 2, 2013 at 1:34 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. construct a model with a ligand (fantasticqhl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 02 Oct 2013 10:04:22 +0200 > From: fantasticqhl <fantasticqhl(a)gmail.com> > To: modeller_usage(a)salilab.org > Subject: [modeller_usage] construct a model with a ligand > Message-ID: <524BD386.4080501(a)gmail.com> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Dear all, > > I am trying to construct a model with a ligand, a zinc ion, but I failed. > > Firstly, I did the alignment with align.py: > > from modeller import * > > env = environ() > aln = alignment(env) > mdl = model(env, file='1ze9', model_segment=('FIRST:A','LAST:A')) > aln.append_model(mdl, align_codes='1ze9A', atom_files='1EZ9.pdb') > aln.append(file='ABCD.ali', align_codes='ABCD') > aln.align2d() > aln.write(file='ABCD-1ze9.ali', alignment_format='PIR') > aln.write(file='ABCD-1ze9.pap', alignment_format='PAP') > align2d.py (END) > > It finished successfully, and I got the aligned ali and pap files: > > ABCD-1ze9.ali: > > >P1;1ze9A > structureX:1ZE9.pdb: 1 :A:+16 :A:::-1.00:-1.00 > DAEFRHDSGYEVHHQK-* > > >P1;ABCD > sequence:ABCD: : : : ::: 0.00: 0.00 > DAEFRHDSGYEVHHQK.* > > ABCD-1ze9.pap > > _aln.pos 10 > 1ze9A DAEFRHDSGYEVHHQK- > ABCD DAEFRHDSGYEVHHQK. > _consrvd * * *** * ** ** ****** > > > The template is a 16-residue peptide coordinate with a zinc ion, which > is residue 17 in the same chain A. The sequence of the unknown structure > is the same as the template's. > This is a test of how to construct a model with a ligand. > > And then I tried to construct the model using model-single.py, which is > the same as the one in the manual: > > > from modeller import * > from modeller.automodel import * > > log.verbose() > env = environ() > env.io.atom_files_directory = ['./:../atom_files'] > > # Read in HETATM records from template PDBs > env.io.hetatm = True > > a = automodel(env, alnfile='ABCD-1ze9.ali', > knowns='1ze9A', sequence='ABCD', > assess_methods=(assess.DOPE, assess.GA341)) > a.starting_model = 1 > a.ending_model = 5 > a.make() > > However, I failed to get the model, I get some error like this: > > File "model-single.py", line 16, in ? > a.make() > File > "/usr/lib/modeller9.11/modlib/modeller/automodel/automodel.py", line 96, > in make > self.homcsr(exit_stage) > File > "/usr/lib/modeller9.11/modlib/modeller/automodel/automodel.py", line > 423, in homcsr > self.check_alignment(aln) > File > "/usr/lib/modeller9.11/modlib/modeller/automodel/automodel.py", line > 405, in check_alignment > aln.check() > File "/usr/lib/modeller9.11/modlib/modeller/alignment.py", > line 197, in check > self.check_structure_structure(io=io) > File "/usr/lib/modeller9.11/modlib/modeller/alignment.py", > line 206, in check_structure_structure > return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) > _modeller.ModellerError: read_te_290E> Number of residues in > the alignment and pdb files are different: 16 17 For alignment > entry: 1 1ze9A > > > Right now, I guess that the error is coming from the alignment, but I > did not find how the alignment was done in the tutorial. So could > someone tell me how to solve this problem? Any suggestions would be > highly appreciated. > > > All the best, > Qinghua > >

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construct a model with a ligand
by fantasticqhl 02 Oct '13

02 Oct '13

Dear all, I am trying to construct a model with a ligand, a zinc ion, but I failed. Firstly, I did the alignment with align.py: from modeller import * env = environ() aln = alignment(env) mdl = model(env, file='1ze9', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='1ze9A', atom_files='1EZ9.pdb') aln.append(file='ABCD.ali', align_codes='ABCD') aln.align2d() aln.write(file='ABCD-1ze9.ali', alignment_format='PIR') aln.write(file='ABCD-1ze9.pap', alignment_format='PAP') align2d.py (END) It finished successfully, and I got the aligned ali and pap files: ABCD-1ze9.ali: >P1;1ze9A structureX:1ZE9.pdb: 1 :A:+16 :A:::-1.00:-1.00 DAEFRHDSGYEVHHQK-* >P1;ABCD sequence:ABCD: : : : ::: 0.00: 0.00 DAEFRHDSGYEVHHQK.* ABCD-1ze9.pap _aln.pos 10 1ze9A DAEFRHDSGYEVHHQK- ABCD DAEFRHDSGYEVHHQK. _consrvd * * *** * ** ** ****** The template is a 16-residue peptide coordinate with a zinc ion, which is residue 17 in the same chain A. The sequence of the unknown structure is the same as the template's. This is a test of how to construct a model with a ligand. And then I tried to construct the model using model-single.py, which is the same as the one in the manual: from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['./:../atom_files'] # Read in HETATM records from template PDBs env.io.hetatm = True a = automodel(env, alnfile='ABCD-1ze9.ali', knowns='1ze9A', sequence='ABCD', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() However, I failed to get the model, I get some error like this: File "model-single.py", line 16, in ? a.make() File "/usr/lib/modeller9.11/modlib/modeller/automodel/automodel.py", line 96, in make self.homcsr(exit_stage) File "/usr/lib/modeller9.11/modlib/modeller/automodel/automodel.py", line 423, in homcsr self.check_alignment(aln) File "/usr/lib/modeller9.11/modlib/modeller/automodel/automodel.py", line 405, in check_alignment aln.check() File "/usr/lib/modeller9.11/modlib/modeller/alignment.py", line 197, in check self.check_structure_structure(io=io) File "/usr/lib/modeller9.11/modlib/modeller/alignment.py", line 206, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 16 17 For alignment entry: 1 1ze9A Right now, I guess that the error is coming from the alignment, but I did not find how the alignment was done in the tutorial. So could someone tell me how to solve this problem? Any suggestions would be highly appreciated. All the best, Qinghua

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