- modeller_usage - salilab.org

parallelization and the master/slaves' env.io.atom_files_directory?
by R K Belew 01 Nov '11

01 Nov '11

i'm separating a script that has worked into separate slave and master modules as described in http://salilab.org/modeller/manual/node435.html. my master script looks like this: > j = job() > j.append(local_slave()) > j.append(local_slave()) > > for afile in alignFiles: > > alnRunDir = '%s%s/' % (dataDir,aname) > if not os.path.isdir(alnRunDir): > print "doAllAlign: Creating directory",alnRunDir > os.makedirs(alnRunDir) > > for runIdx in range(nruns): > j.queue_task(SeedTask(argumentList)) > > for result in j.yield_tasks_unordered(): > print result and my slave task like this: > class SeedTask(task): > """A task to read in a PDB file on the slave, and return the resolution""" > > def run(self,dataDir,afile,aname,runIdx,randMethod,knownLbl,seqLbl,nmodPerRun,atomDeviation ): > env = environ() > env.io.atom_files_directory = [dataDir] > arg4seed = - (int(runIdx) + 2) > env = environ(arg4seed) > > runDir = '%s/%s/run_%02d/' % (dataDir,aname,runIdx) > if not os.path.isdir(runDir): > print "doAllAlign: Creating directory",runDir > os.makedirs(runDir) > > os.chdir(runDir) > > a = automodel(env, alnfile=afile, > knowns=knownLbl, sequence=seqLbl, > assess_methods=(assess.DOPE, assess.GA341)) > > a.starting_model = 1 > # 2do: test task / run ratio? > a.ending_model = nmodPerRun > > a.deviation = atomDeviation > if randMethod=='XYZ': > a.rand_method = randomize.xyz > elif randMethod=='DIHEDRAL': > a.rand_method = randomize.dihedrals > > a.make() i'm stepping thru with a debugger, and it gets to the yield_tasks_unordered() generator in the master. but as i attempt to make the next step it throws an exception that seems to have to do with env.io.atom_files_directory now (in the master/slave version) not getting set correctly? > Running 14 tasks on 2 slaves > /usr/bin/python2.6 /usr/lib/modeller9.10/bin/modslave.py -slave 127.0.1.1:59861:0:BGRESKQY >& seed_align_pp.slave0 > /usr/bin/python2.6 /usr/lib/modeller9.10/bin/modslave.py -slave 127.0.1.1:59861:1:ZCQMRSNQ >& seed_align_pp.slave1 > Identified slave <Slave on localhost> > Identified slave <Slave on localhost> > Traceback (most recent call last): > File "/home/rik/Data/pkg/eclipse/plugins/org.python.pydev.debug_2.2.3.2011100616/pysrc/pydevd.py", line 1267, in <module> > debugger.run(setup['file'], None, None) > File "/home/rik/Data/pkg/eclipse/plugins/org.python.pydev.debug_2.2.3.2011100616/pysrc/pydevd.py", line 1020, in run > pydev_imports.execfile(file, globals, locals) #execute the script > File "/home/rik/Code/eclipse/modeller/src/seed_align_pp.py", line 98, in <module> > doAllAlign() > File "/home/rik/Code/eclipse/modeller/src/seed_align_pp.py", line 91, in doAllAlign > for result in j.yield_tasks_unordered(): > File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 146, in yield_tasks_unordered > for task in self._finish_all_tasks(): > File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 164, in _finish_all_tasks > task = self._process_event(obj, s) > File "/usr/lib/python2.6/dist-packages/modeller/parallel/job.py", line 180, in _process_event > task = obj.task_results() > File "/usr/lib/python2.6/dist-packages/modeller/parallel/slave.py", line 61, in task_results > r = self.get_data(allow_heartbeat=True) > File "/usr/lib/python2.6/dist-packages/modeller/parallel/communicator.py", line 89, in get_data > (cmdtype, obj) = self._recv() > File "/usr/lib/python2.6/dist-packages/modeller/parallel/communicator.py", line 130, in _recv > raise RemoteError(obj.exc, self) > modeller.parallel.communicator.RemoteError: <type 'IOError'>: pdbnam_____E> Filename for PDB code not found: 1A04A.pdb > Directories: > Extensions : :.atm:.pdb:.ent:.crd > (Also tried prepending 'pdb', looking for .Z, .gz, .bz2, .7z, .xz, > and trying PDB-style subdirectories - e.g. ab for pdb1abc.ent) > from <Slave on localhost> would you know what i'm doing wrong here? thanks again for your help. Rik

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automodel.max_molpdf recommended values and usage format
by Andrew Voronkov 01 Nov '11

01 Nov '11

Dear Modeller users, how on your opinion modeller objective function correlates with quality of the models. For example I have objective function value 1730 for one modelk and -750 which as I understand reflects free energy. Does it mean that I shouldn t consider the first one at all? Let's say I want to make cutoff -100 for the objective function. In which format it should be done? automodel.max_molpdf -100 is that correct? Sincerely yours, Andrey

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 134
by Ashish Runthala 01 Nov '11

01 Nov '11

Dear Alex, It is pretty simple. Simplest way is to make the alignment file with your loop region well aligned to corresponding chunk in structure B and for other residues, put gap in your alignment file for structure A, corresponding to respective additional residues in structure B. You may use the PRALINE alignment to do it and pipeline that to MODELLER. There is one more way too to consider the environmental effects on structural topology of A as per the structure B. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Tuesday, November 1, 2011 9:31:40 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 134 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. Homology Modeling of the Loop (Alexander Predeus) 2. Re: modeller_usage Digest, Vol 10, Issue 132 (Ashish Runthala) ---------------------------------------------------------------------- Message: 1 Date: Mon, 31 Oct 2011 15:02:46 -0400 From: Alexander Predeus <predeus(a)gmail.com> Subject: [modeller_usage] Homology Modeling of the Loop To: modeller_usage(a)salilab.org Message-ID: <CADvsxO=iHEGXCyUW=DfC7GrRumcYcfgUYxmp5gnPjGC5Cff73w(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, I'm very much a beginner at modeling, and this question might be very trivial. I hope you still would hint me about the answer, for it would help me a lot. I have a large protein (say 1500 residues, let's call it protein A) and its homologue (protein B) of about the same size. Both proteins have published crystal structures. Both proteins have a key structural element, loop L. The loop is poorly resolved in structure A, but well resolved in homologous structure B. Now, I can take just the L loop regions as separate PDB files from both A and B and do homology modeling of A based on B; this works really well. But I also would like the model to consider the surroundings (the rest of the structure) when evaluating the energies. Thus, I'd like to keep the REST of A's crystal structure intact, and only model loop L based on the structure of the same region in protein B. How can I achieve that? Thank you in advance! - Alex Predeus Michigan State University

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 132
by Ashish Runthala 31 Oct '11

31 Oct '11

Dear Junior, What you actually want to state? Do you need to build an average model based on the topology of 10 models? For this you may use them as templates without calling the chain identifiers. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Monday, October 31, 2011 7:46:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 132 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. Re: What is the mistake in this set of lines? (Ashish Runthala) 2. Re: What is the mistake in this set of lines? (Ashish Runthala) 3. Build a model with multiple models (junior) ---------------------------------------------------------------------- Message: 1 Date: Sat, 29 Oct 2011 10:39:22 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Subject: Re: [modeller_usage] What is the mistake in this set of lines? To: modeller <modeller_usage(a)salilab.org> Message-ID: <20822758.298281319864962852.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 Is it possible that i can declare some variables in python similar to the standard default MODELLER variables atomfile, pdbfile and code. How these variables are declared in MODELLER? Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "Ashish Runthala" <ashishr(a)bits-pilani.ac.in> To: "modeller" <modeller_usage(a)salilab.org> Sent: Friday, October 28, 2011 8:17:00 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: What is the mistake in this set of lines? Dear Modellers, I wrote a script to do three template modeling for a target sequence from all the templates present in the same folder. The script is expected to take 1SHW, 1SHX fixed and the third one should be iteratively taken from the current folder. MODELLER defines atom as any PDB or .atm template file and pdbfile is the keyword defined for template with chain ID. So when i use pdbfile for both 1SHW, 1SHX why it only takes the one with the 2nd entry. Like a normal variable initial template name changes when it is assigned to some other template. So what is the mistake in this set of lines? How should i solve this task. for (code, code, atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'), (pdbfile,pdbfile,fileName,'A')): mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=atomfile) Thanks, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 2 Date: Sun, 30 Oct 2011 15:52:37 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Subject: Re: [modeller_usage] What is the mistake in this set of lines? To: modeller <modeller_usage(a)salilab.org> Message-ID: <15487763.309941319970157647.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 What nobody knows to declare such data types? Any guesses with anyone what it should be, as probably there in MODELLER modules and functional binaries. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "Ashish Runthala" <ashishr(a)bits-pilani.ac.in> To: "modeller" <modeller_usage(a)salilab.org> Sent: Saturday, October 29, 2011 10:39:22 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Re: What is the mistake in this set of lines? Is it possible that i can declare some variables in python similar to the standard default MODELLER variables atomfile, pdbfile and code. How these variables are declared in MODELLER? Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "Ashish Runthala" <ashishr(a)bits-pilani.ac.in> To: "modeller" <modeller_usage(a)salilab.org> Sent: Friday, October 28, 2011 8:17:00 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: What is the mistake in this set of lines? Dear Modellers, I wrote a script to do three template modeling for a target sequence from all the templates present in the same folder. The script is expected to take 1SHW, 1SHX fixed and the third one should be iteratively taken from the current folder. MODELLER defines atom as any PDB or .atm template file and pdbfile is the keyword defined for template with chain ID. So when i use pdbfile for both 1SHW, 1SHX why it only takes the one with the 2nd entry. Like a normal variable initial template name changes when it is assigned to some other template. So what is the mistake in this set of lines? How should i solve this task. for (code, code, atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'), (pdbfile,pdbfile,fileName,'A')): mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=atomfile) Thanks, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 3 Date: Mon, 31 Oct 2011 06:16:22 -0800 From: junior <sam.kauba(a)gmail.com> Subject: [modeller_usage] Build a model with multiple models To: modeller_usage(a)salilab.org Message-ID: <CAEJMx6wtgQ8U6MAG+uepWiwwcvTHbCvqFZ824_jJJS3cM2jciQ(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi, How do I build a PDB file containing more than 10 models? Thank you. Sam Kauba ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 10, Issue 132 ***********************************************

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Re: [modeller_usage] What is the mistake in this set of lines
by Igor Dvortsov 31 Oct '11

31 Oct '11

>for (code, code, atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'), > (pdbfile,pdbfile,fileName,'A')): > mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) > aln.append_model(mdl, atom_files=code, align_codes=atomfile) it's python question, not modeller. your for-cycle executes 2 times, in first run code=1SHWA, then code=1SHXA, atomfile=1SHX, chan=A and body of for-cycle executed, in second run code=pdbfile, atomfile=fileName,chain=A. if you have variables pdbfile and fileName as strings defined, the body of for-cycle will be executed again. it seems, this is not that you supposed. maybe, something like this atomfile='1SHX' for (code,chain) in (('1SHWA','A'),('1SHXA','A')): mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=atomfile) kind regards, Igor modeller_usage-request(a)salilab.org пишет: > 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. Re: What is the mistake in this set of lines? (Ashish Runthala) > 2. Re: What is the mistake in this set of lines? (Ashish Runthala) > 3. Build a model with multiple models (junior) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 29 Oct 2011 10:39:22 +0530 (IST) > From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> > Subject: Re: [modeller_usage] What is the mistake in this set of > lines? > To: modeller <modeller_usage(a)salilab.org> > Message-ID: > <20822758.298281319864962852.JavaMail.root(a)mailserver.bits-pilani.ac.in> > > Content-Type: text/plain; charset=utf-8 > > Is it possible that i can declare some variables in python similar to the standard default MODELLER variables atomfile, pdbfile and code. > How these variables are declared in MODELLER? > > Thanks > Ashish > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > ----- Original Message ----- > From: "Ashish Runthala" <ashishr(a)bits-pilani.ac.in> > To: "modeller" <modeller_usage(a)salilab.org> > Sent: Friday, October 28, 2011 8:17:00 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi > Subject: What is the mistake in this set of lines? > > Dear Modellers, > I wrote a script to do three template modeling for a target sequence from all the templates present in the same folder. > The script is expected to take 1SHW, 1SHX fixed and the third one should be iteratively taken from the current folder. > > MODELLER defines atom as any PDB or .atm template file and pdbfile is the keyword defined for template with chain ID. > So when i use pdbfile for both 1SHW, 1SHX why it only takes the one with the 2nd entry. Like a normal variable initial template name changes when it is assigned to some other template. > > So what is the mistake in this set of lines? How should i solve this task. > > for (code, code, atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'), > (pdbfile,pdbfile,fileName,'A')): > mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) > aln.append_model(mdl, atom_files=code, align_codes=atomfile) > > > > Thanks, > Ashish > > > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > > ------------------------------ > > Message: 2 > Date: Sun, 30 Oct 2011 15:52:37 +0530 (IST) > From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> > Subject: Re: [modeller_usage] What is the mistake in this set of > lines? > To: modeller <modeller_usage(a)salilab.org> > Message-ID: > <15487763.309941319970157647.JavaMail.root(a)mailserver.bits-pilani.ac.in> > > Content-Type: text/plain; charset=utf-8 > > What nobody knows to declare such data types? Any guesses with anyone what it should be, as probably there in MODELLER modules and functional binaries. > > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > ----- Original Message ----- > From: "Ashish Runthala" <ashishr(a)bits-pilani.ac.in> > To: "modeller" <modeller_usage(a)salilab.org> > Sent: Saturday, October 29, 2011 10:39:22 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi > Subject: Re: What is the mistake in this set of lines? > > Is it possible that i can declare some variables in python similar to the standard default MODELLER variables atomfile, pdbfile and code. > How these variables are declared in MODELLER? > > Thanks > Ashish > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > ----- Original Message ----- > From: "Ashish Runthala" <ashishr(a)bits-pilani.ac.in> > To: "modeller" <modeller_usage(a)salilab.org> > Sent: Friday, October 28, 2011 8:17:00 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi > Subject: What is the mistake in this set of lines? > > Dear Modellers, > I wrote a script to do three template modeling for a target sequence from all the templates present in the same folder. > The script is expected to take 1SHW, 1SHX fixed and the third one should be iteratively taken from the current folder. > > MODELLER defines atom as any PDB or .atm template file and pdbfile is the keyword defined for template with chain ID. > So when i use pdbfile for both 1SHW, 1SHX why it only takes the one with the 2nd entry. Like a normal variable initial template name changes when it is assigned to some other template. > > So what is the mistake in this set of lines? How should i solve this task. > > for (code, code, atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'), > (pdbfile,pdbfile,fileName,'A')): > mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) > aln.append_model(mdl, atom_files=code, align_codes=atomfile) > > > > Thanks, > Ashish > > > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > > ------------------------------ > > Message: 3 > Date: Mon, 31 Oct 2011 06:16:22 -0800 > From: junior <sam.kauba(a)gmail.com> > Subject: [modeller_usage] Build a model with multiple models > To: modeller_usage(a)salilab.org > Message-ID: > <CAEJMx6wtgQ8U6MAG+uepWiwwcvTHbCvqFZ824_jJJS3cM2jciQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > > How do I build a PDB file containing more than 10 models? > > > Thank you. > > > > Sam Kauba > > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 10, Issue 132 > *********************************************** > > >

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Re: [modeller_usage] Build a model with multiple models
by Mensur Dlakic 31 Oct '11

31 Oct '11

I am assuming you have two lines in your script that look something like this: a.starting_model= 1 a.ending_model = 10 Just put the larger number in place of 10 on the second line. Alternatively, you could change the seed number (the line is something like environ(rand_seed = -57693) and run the same script multiple times to generate the desired number of models. The problem there is that files would have to be renamed after each run to not be overwritten in the next run, so I'd still go with first suggestion. At 08:16 AM 10/31/2011, you wrote: >Hi, > > >How do I build a PDB file containing more than 10 models? > > >Thank you. > > > >Sam Kauba >_______________________________________________ >modeller_usage mailing list >modeller_usage(a)salilab.org >https://salilab.org/mailman/listinfo/modeller_usage ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

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What is the mistake in this set of lines?
by Ashish Runthala 30 Oct '11

30 Oct '11

Dear Modellers, I wrote a script to do three template modeling for a target sequence from all the templates present in the same folder. The script is expected to take 1SHW, 1SHX fixed and the third one should be iteratively taken from the current folder. MODELLER defines atom as any PDB or .atm template file and pdbfile is the keyword defined for template with chain ID. So when i use pdbfile for both 1SHW, 1SHX why it only takes the one with the 2nd entry. Like a normal variable initial template name changes when it is assigned to some other template. So what is the mistake in this set of lines? How should i solve this task. for (code, code, atomfile, chain) in (('1SHWA','1SHXA','1SHX','A'), (pdbfile,pdbfile,fileName,'A')): mdl = model(env, file=atomfile, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=atomfile) Thanks, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 130
by Ashish Runthala 28 Oct '11

28 Oct '11

Dear Andrew, That is correct. But the ligand entity must be with biologically correct topology orientation, applicability and feasible conformation surface. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Friday, October 28, 2011 8:36:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 130 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. Re: modeller_usage Digest, Vol 10, Issue 124 (Andrew Voronkov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 28 Oct 2011 15:54:44 +0400 From: Andrew Voronkov <drugdesign(a)yandex.ru> Subject: Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 124 To: modeller_usage(a)salilab.org Message-ID: <458201319802884(a)web59.yandex.ru> Content-Type: text/plain; charset=koi8-r In general the transfer of ligand with remaning flexibility shoud imitaqte such induced fit, right? Best regards, Andrew 21.10.2011, 14:40, modeller_usage-request(a)salilab.org: > 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. Re: modeller_usage Digest, Vol 10, Issue 123 (Ashish Runthala) > ???2. induced fit modeling by Modeller or ModLoop (Andrew Voronkov) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Oct 2011 16:17:34 +0530 (IST) > From: Ashish Runthala ?<ashishr(a)bits-pilani.ac.in> > Subject: Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 123 > To: modeller usage <modeller_usage(a)salilab.org> > Message-ID: > ????????<8607667.201091319021254484.JavaMail.root(a)mailserver.bits-pilani.ac.in> > > Content-Type: text/plain; charset=utf-8 > > Sir Ben is correct. But there is an option to let your model be biased to its actual native state, instead of forcing it to the topology of your templates. > Select good templates which you might have already done correctly. > Now if you know how to make a correct representative alignment for your target, that is the best choice. > Or if you don't try to harness continuous or discontinuous reliable structural folds from templates as per your constraints. > Don't rely simply on MD to relax the models. If your first model is distant from its native state, no way you can pull it through. So focus on template selection and correct alignment to build your model through these reliable scaffolds. > > Good Luck > Ashish > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > ----- Original Message ----- > From: "modeller usage-request" <modeller_usage-request(a)salilab.org> > To: "modeller usage" <modeller_usage(a)salilab.org> > Sent: Wednesday, October 19, 2011 12:12:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi > Subject: modeller_usage Digest, Vol 10, Issue 123 > > 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. Re: Modeling GPCRs (Modeller Caretaker) > ???2. Re: Modeling GPCRs (Hugo Gutierrez de Teran) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 18 Oct 2011 17:52:46 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] Modeling GPCRs > To: Maggie Pruitt <mamdahl(a)iastate.edu> > Cc: modeller_usage(a)salilab.org > Message-ID: <4E9E1F5E.8010507(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 10/18/11 1:57 PM, Maggie Pruitt wrote: > >> ?I am interested in using Modeller for predicting the structure of the G >> ?protein-coupled receptor I study. This protein does not have any >> ?homologous proteins in the PDB database and there is no experimental >> ?data to help model the protein. Knowing this, can Modeller provide an >> ?accurate structure of my protein to use in molecular dynamics >> ?simulations? I understand that I can choose other crystallized GPCRs to >> ?use as templates, but I am concerned that since Modeller is a homology >> ?modeling program that the end model would simply look like my protein >> ?forced onto the template structure. > > Yes, you are exactly correct. Modeller is not limited to using homologs > as templates; it can use any protein that you believe is structurally > similar to the protein you intend to model. But if you choose a template > that is not similar, you will likely get a poor model. > > ????????Ben Webb, Modeller Caretaker > > -- > modeller-care(a)salilab.org ????????????http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > ------------------------------ > > Message: 2 > Date: Wed, 19 Oct 2011 08:42:21 +0200 > From: Hugo Gutierrez de Teran <hugo.teran(a)usc.es> > Subject: Re: [modeller_usage] Modeling GPCRs > To: modeller_usage(a)salilab.org > Message-ID: > <CAG02diR1jQJizHkK4vM0RQm+VaCg0zke_QYMAT_8fPiDtJp6vg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Maggie, > > We have developed GPCRModSim, a web server that facilitates the process of > modeling GPCRs using Modeller as a back end modeling tool ( > http://gpcr.usc.es) > In particular, once you upload your sequence or swissprot code, you will get > an optimized alignment with all crystallized GPCRs (you can choose also > between templates in the active or inactive conformations). The server will > recommend you the most suitable template based on TM homologies, although > you can further inspect this and change the default selection on the basis > of homologies between particular regions. > > Please visit http://gpcr.usc.es > > For a test case, the H1 histamine receptor modeled with excelent accuracy, > see the tutorial at http://gpcr.usc.es/tutorial > > There are several other features, like the possibility of loop refinement > (using loopmodel routines) and the MD simulation of your simulated model in > an atomistic model of the membrane (using GROMACS routines). > > Hugo > > -- > Hugo G. de Teran, PhD. > "Parga Pondal" Research fellow > Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS > Santiago de Compostela (SPAIN) > > Phone +34 881813873 > e-mail:hugo.teran@usc.es ??????http://webspersoais.usc.es/hugo.teran > > 2011/10/18 Maggie Pruitt <mamdahl(a)iastate.edu> > >> ?Hello, >> >> I am interested in using Modeller for predicting the structure of the G >> protein-coupled receptor I study. ?This protein does not have any homologous >> proteins in the PDB database and there is no experimental data to help model >> the protein. ?Knowing this, can Modeller provide an accurate structure of my >> protein to use in molecular dynamics simulations? ?I understand that I can >> choose other crystallized GPCRs to use as templates, but I am concerned that >> since Modeller is a homology modeling program that the end model would >> simply look like my protein forced onto the template structure.**** >> >> If anyone can give me some further insight on this manner, I would greatly >> appreciate it. >> >> Thanks in advance for your help! >> >> Sincerely, >> >> Maggie >> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage(a)salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >> >> > > -- > > -- > Hugo G. de Teran, PhD. > "Parga Pondal" Research fellow > Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS > Santiago de Compostela (SPAIN) > > Phone +34 881813873 > e-mail:hugo.teran@usc.es ??????http://webspersoais.usc.es/hugo.teran > > -- > > -- > Hugo G. de Teran, PhD. > "Parga Pondal" Research fellow > Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS > Santiago de Compostela (SPAIN) > > Phone +34 881813873 > e-mail:hugo.teran@usc.es ??????http://webspersoais.usc.es/hugo.teran >

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 124
by Andrew Voronkov 28 Oct '11

28 Oct '11

In general the transfer of ligand with remaning flexibility shoud imitaqte such induced fit, right? Best regards, Andrew 21.10.2011, 14:40, modeller_usage-request(a)salilab.org: > 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. Re: modeller_usage Digest, Vol 10, Issue 123 (Ashish Runthala) > 2. induced fit modeling by Modeller or ModLoop (Andrew Voronkov) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Oct 2011 16:17:34 +0530 (IST) > From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> > Subject: Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 123 > To: modeller usage <modeller_usage(a)salilab.org> > Message-ID: > <8607667.201091319021254484.JavaMail.root(a)mailserver.bits-pilani.ac.in> > > Content-Type: text/plain; charset=utf-8 > > Sir Ben is correct. But there is an option to let your model be biased to its actual native state, instead of forcing it to the topology of your templates. > Select good templates which you might have already done correctly. > Now if you know how to make a correct representative alignment for your target, that is the best choice. > Or if you don't try to harness continuous or discontinuous reliable structural folds from templates as per your constraints. > Don't rely simply on MD to relax the models. If your first model is distant from its native state, no way you can pull it through. So focus on template selection and correct alignment to build your model through these reliable scaffolds. > > Good Luck > Ashish > > Ashish Runthala, > Lecturer, Structural Biology Cell, > Biological Sciences Group, > BITS, Pilani > Rajasthan, INDIA > > ----- Original Message ----- > From: "modeller usage-request" <modeller_usage-request(a)salilab.org> > To: "modeller usage" <modeller_usage(a)salilab.org> > Sent: Wednesday, October 19, 2011 12:12:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi > Subject: modeller_usage Digest, Vol 10, Issue 123 > > 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. Re: Modeling GPCRs (Modeller Caretaker) > 2. Re: Modeling GPCRs (Hugo Gutierrez de Teran) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 18 Oct 2011 17:52:46 -0700 > From: Modeller Caretaker <modeller-care(a)salilab.org> > Subject: Re: [modeller_usage] Modeling GPCRs > To: Maggie Pruitt <mamdahl(a)iastate.edu> > Cc: modeller_usage(a)salilab.org > Message-ID: <4E9E1F5E.8010507(a)salilab.org> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 10/18/11 1:57 PM, Maggie Pruitt wrote: > >> I am interested in using Modeller for predicting the structure of the G >> protein-coupled receptor I study. This protein does not have any >> homologous proteins in the PDB database and there is no experimental >> data to help model the protein. Knowing this, can Modeller provide an >> accurate structure of my protein to use in molecular dynamics >> simulations? I understand that I can choose other crystallized GPCRs to >> use as templates, but I am concerned that since Modeller is a homology >> modeling program that the end model would simply look like my protein >> forced onto the template structure. > > Yes, you are exactly correct. Modeller is not limited to using homologs > as templates; it can use any protein that you believe is structurally > similar to the protein you intend to model. But if you choose a template > that is not similar, you will likely get a poor model. > > Ben Webb, Modeller Caretaker > > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > ------------------------------ > > Message: 2 > Date: Wed, 19 Oct 2011 08:42:21 +0200 > From: Hugo Gutierrez de Teran <hugo.teran(a)usc.es> > Subject: Re: [modeller_usage] Modeling GPCRs > To: modeller_usage(a)salilab.org > Message-ID: > <CAG02diR1jQJizHkK4vM0RQm+VaCg0zke_QYMAT_8fPiDtJp6vg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Maggie, > > We have developed GPCRModSim, a web server that facilitates the process of > modeling GPCRs using Modeller as a back end modeling tool ( > http://gpcr.usc.es) > In particular, once you upload your sequence or swissprot code, you will get > an optimized alignment with all crystallized GPCRs (you can choose also > between templates in the active or inactive conformations). The server will > recommend you the most suitable template based on TM homologies, although > you can further inspect this and change the default selection on the basis > of homologies between particular regions. > > Please visit http://gpcr.usc.es > > For a test case, the H1 histamine receptor modeled with excelent accuracy, > see the tutorial at http://gpcr.usc.es/tutorial > > There are several other features, like the possibility of loop refinement > (using loopmodel routines) and the MD simulation of your simulated model in > an atomistic model of the membrane (using GROMACS routines). > > Hugo > > -- > Hugo G. de Teran, PhD. > "Parga Pondal" Research fellow > Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS > Santiago de Compostela (SPAIN) > > Phone +34 881813873 > e-mail:hugo.teran@usc.es http://webspersoais.usc.es/hugo.teran > > 2011/10/18 Maggie Pruitt <mamdahl(a)iastate.edu> > >> Hello, >> >> I am interested in using Modeller for predicting the structure of the G >> protein-coupled receptor I study. This protein does not have any homologous >> proteins in the PDB database and there is no experimental data to help model >> the protein. Knowing this, can Modeller provide an accurate structure of my >> protein to use in molecular dynamics simulations? I understand that I can >> choose other crystallized GPCRs to use as templates, but I am concerned that >> since Modeller is a homology modeling program that the end model would >> simply look like my protein forced onto the template structure.**** >> >> If anyone can give me some further insight on this manner, I would greatly >> appreciate it. >> >> Thanks in advance for your help! >> >> Sincerely, >> >> Maggie >> >> _______________________________________________ >> modeller_usage mailing list >> modeller_usage(a)salilab.org >> https://salilab.org/mailman/listinfo/modeller_usage >> >> > > -- > > -- > Hugo G. de Teran, PhD. > "Parga Pondal" Research fellow > Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS > Santiago de Compostela (SPAIN) > > Phone +34 881813873 > e-mail:hugo.teran@usc.es http://webspersoais.usc.es/hugo.teran > > -- > > -- > Hugo G. de Teran, PhD. > "Parga Pondal" Research fellow > Fundaci?n P?blica Galega de Medicina Xen?mica - SERGAS > Santiago de Compostela (SPAIN) > > Phone +34 881813873 > e-mail:hugo.teran@usc.es http://webspersoais.usc.es/hugo.teran >

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Restraint conversion
by Matthias Schmidt 27 Oct '11

27 Oct '11

Hi, Are there tools or scripts out there that can convert Modeller restraints (eg. rsr files) to Gromacs distance restraints? If not, how would you go at it? Best, Matthias -- Structural Bioinformatics and Computational Biochemistry Unit Dept. of Biochemistry University of Oxford http://sbcb.bioch.ox.ac.uk/schmidt.php

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