- modeller_usage - salilab.org

Modeller 9.11 release
by Modeller Caretaker 06 Sep '12

06 Sep '12

The new version of Modeller, 9.11, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.11 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.11 is primarily a bugfix release relative to the last public release (9.10). Major user-visible changes include: # Alpha (Tru64), Itanium (ia64) and Sun Solaris binaries are no longer provided. If you wish to use Modeller on one of these machines, please use the older 9.10 version. # sequence_db objects now only store part of the sequence database in memory when using a binary (HDF5) file (databases in PIR or FASTA format still must be read in in their entirety). Functions that use sequence databases now take a window_size argument, that controls how much of the database is read into memory at one time. This results in much lower memory usage when using large databases such as UniProt. # SSBOND and CONECT records are now written to PDB files when models containing disulfides are saved. # The default behavior of automatically converting common modified residues (MSE, MEX, ABU) to their standard equivalents can now be disabled by setting env.io.convert_modres=False. See the Modeller manual for a full change log: http://salilab.org/modeller/9.11/manual/node39.html If you encounter bugs in Modeller 9.11, please see http://salilab.org/modeller/9.11/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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minimize after filling the gaps
by Mary Varughese 06 Sep '12

06 Sep '12

Hi, On building the missing residues in a protein(under the option no change to rest of the protein), could i retain the cofactors. Should i minimize the protein as a whole or build region specifically before performing any docking and simulation. I understand the building process itself perform some minimization. Isn't that enough? Thanking You, -- Mary Varughese Research Scholar School of Pure and Applied Physics Mahatma Gandhi University India

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Re: [modeller_usage] Trouble with angle restrain in chimera
by virginia miguel 04 Sep '12

04 Sep '12

João! Thank you very much for your help! that work out! Sorry to bother you again but now the error that appears is the following: File "model-multiple.py", line 17, in special_restraints feature=features.angle(a['CA:796'], TypeError: unsubscriptable object For what i can understand it does not recognize a sequence of atoms in class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms f = forms.gaussian(group=physical.angle, feature=features.angle(a['CA:796'], a['CA:822'], a['CA:855']), mean=2.827, stdev=0.010) I have tried feature=features.angle(a['CA:796', 'CA:822','CA:855']), and feature=features.angle(a 'CA:796', 'CA:822','CA:855' ), but they did not worked. Do you know how could I fix this? I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) --- El lun 3-sep-12, João Rodrigues <anaryin(a)gmail.com> escribió: De: João Rodrigues <anaryin(a)gmail.com> Asunto: Re: [modeller_usage] Trouble with angle restrain in chimera Para: "virginia miguel" <virgimiguel(a)yahoo.com.ar> Cc: modeller_usage(a)salilab.org Fecha: lunes, 3 de septiembre de 2012, 17:24 Hey Virginia, You have one less indentation level in that line. Python then considers it out of the class MyModel and thus, rsr is not previously declared. Just hit tab/4 spaces behind rsr.add and it should work. Best, João No dia 3 de Set de 2012 22:45, "virginia miguel" <virgimiguel(a)yahoo.com.ar> escreveu: Hi everyone, I am trying to build a chimera protein based on two known structures that do not overlap, and I am trying to specify an angle restrain between the two domains that are model to give information of their relative orientation obtained experimentally using this script: # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms f = forms.gaussian(group=physical.angle, feature=features.angle(a['CA:796'], a['CA:822'], a['CA:855']), mean=2.827, stdev=0.010) rsr.add(f) a = MyModel(env, alnfile = 'align2.ali', # alignment filename knowns = ('2OK2','1FW6','1E3M'), # codes of the templates sequence = 'PAOI') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 50 # index of the last model # (determines how many models to calculate) a.make() but I get this error: File "model-multiple.py", line 12, in ? class MyModel(automodel): File "model-multiple.py", line 21, in MyModel rsr.add(f) NameError: name 'rsr' is not defined So I do not know what I am missing....if someone can help me! Thank you in advance! Virginia. I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White) _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage -----Adjunto en línea a continuación----- _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage

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Trouble with angle restrain in chimera
by virginia miguel 03 Sep '12

03 Sep '12

Hi everyone, I am trying to build a chimera protein based on two known structures that do not overlap, and I am trying to specify an angle restrain between the two domains that are model to give information of their relative orientation obtained experimentally using this script: # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms f = forms.gaussian(group=physical.angle, feature=features.angle(a['CA:796'], a['CA:822'], a['CA:855']), mean=2.827, stdev=0.010) rsr.add(f) a = MyModel(env, alnfile = 'align2.ali', # alignment filename knowns = ('2OK2','1FW6','1E3M'), # codes of the templates sequence = 'PAOI') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 50 # index of the last model # (determines how many models to calculate) a.make() but I get this error: File "model-multiple.py", line 12, in ? class MyModel(automodel): File "model-multiple.py", line 21, in MyModel rsr.add(f) NameError: name 'rsr' is not defined So I do not know what I am missing....if someone can help me! Thank you in advance! Virginia. I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)

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GNUPLOT using the command please sent to email , how to use gnuplot
by Nandha Kumar 30 Aug '12

30 Aug '12

-- nandhakumar

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modeller9.10 using error on display
by Nandha Kumar 24 Aug '12

24 Aug '12

cannot open logfile script1.log;permission denied ( please sent solutions) i am using windows 8 os ,python 3.2.3 installed ) -- nandhakumar

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Modelling a heterodimeric structure using heterodimeric template
by Rakshambikai R 17 Aug '12

17 Aug '12

Dear Sir/Madam, I am modelling a heterodimeric structure from a heterodimeric template. I tried modelling it using separate chains but I am facing difficulty in building the complex. Is it possible to build a model using the complex structure as a whole (I did see a mention of using "/" as a chain separater in your archives for a homodimer)? If so, how do I specify the regions to be modelled?I have put an example of the regions: query chain 1 length: 878 region aligning:1-827 template: chain B; actual region in pdb: 362-1335 ; region aligning;427-1335 query chain 2: length: 901 length aligning:59-848 template: chain A; actual region in pdb:1-855; length aligning;150-854 Awaiting your response. Thanking you, RAKSHAMBIKAI R PhD student Prof N Srinivasan's lab MBU,IISc Ph:080-22932837 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Membrane environment
by Marco Lolicato 13 Aug '12

13 Aug '12

Dear users, I've already had a look into the forum but I didn't find the answer. I would like to model a chimera protein where the two segments are deposited into the Protein DataBank. One of the two proteins is a membrane protein. I used the default values with really interesting results, but I guess I have a problem in modeling the soluble portion of the chimera: in fact, in the model, it appear in the same orientation of the transmembrane helices of the membrane portion. It seems that the soluble portion itself can insert in the membrane. Are there any restraints on membrane protein to add to my default script? Or, do you have any suggestion to overcome the bias? Could I include a special "membrane environment" in the calculation? Thank you for your time, Marco -- Dr. Marco Lolicato, PhD. Università degli Studi di Milano Dip. Biologia - Sez. Biochimica e Fisiologia delle Piante Via Celoria, 26 20133 Milano Italy

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regarding Dope score in optimize.py
by NUTAN CHAUHAN 13 Aug '12

13 Aug '12

Hallo all, I have mutated my protein using mutate_selection.py and optimized it using optimize.py. Optimize.py is giving me 5 models..but I don't know on what basis i should chose the best. Can I use Dope and molpdf score for the same? How can I these by running optimize.py? thanks in advance. Ragards, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand ________________________________ From: "modeller_usage-request(a)salilab.org" <modeller_usage-request(a)salilab.org> To: modeller_usage(a)salilab.org Sent: Wednesday, 16 May 2012 6:47 AM Subject: modeller_usage Digest, Vol 11, Issue 58 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 different conformations of a protein from related structures (Modeller Caretaker) 2. Regarding Constraints covered in the Salign_Multiple_Struc.py (Ashish Runthala) 3. Re: Regarding Constraints covered in the Salign_Multiple_Struc.py (Ashish Runthala) 4. modeller.parallel.communicator.RemoteError (Xiao-Ping Zhang) ---------------------------------------------------------------------- Message: 1 Date: Mon, 07 May 2012 08:06:04 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: EGY <mp.2egy(a)gmail.com> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] modeling different conformations of a protein from related structures Message-ID: <4FA7E4DC.7070200(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/7/12 7:35 AM, EGY wrote: > Sorry, my question is much more elementary. Your original question was addressed just last week on the mailing list: http://salilab.org/archives/modeller_usage/2012/msg00152.html > I see an example from the tutorial (Advanced Modeling, Modeling > ligands in the binding site) on an alignment similar to what I want. > However, I don't see the associated script to give this alignment You make the alignment yourself, e.g. in a text editor. There is no script to generate it for you automatically. > In this example, only the binding pocket of the 1emd structure was > included in the alignment. I would also need to know how not to > include a region in one of the other sequences. Either edit the PDB file to remove the region you don't want to include, or see http://salilab.org/modeller/9.10/FAQ.html#2 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, 9 May 2012 12:14:41 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> To: modeller <modeller_usage(a)salilab.org> Subject: [modeller_usage] Regarding Constraints covered in the Salign_Multiple_Struc.py Message-ID: <2636755.831336545880971.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 Dear Modellers, Tell me a preliminary aspect of the script Salign_Multiple_Struc.py If multiple local folds are present in the computed alignment of this script for different templates, something like this, Template1>---AAAAAA---BBBBBBBB----* Template2>--APPPAAA---BCBBBB------* Template3>----AAA----BBBBBBBB-----* Template4>----AA-------BB---------* Elaborate the factors considered by MODELLER to put template2 close to the template1, and why template3 and 4 are kept away from template1 and closer to template2. Is it minimal RMSD of local template chunks, equal chunk lengths or something else. Give me the complete list of the considered factors considered in MODELLER for such a computation. Best Regards Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 3 Date: Sun, 13 May 2012 20:06:23 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> To: modeller <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] Regarding Constraints covered in the Salign_Multiple_Struc.py Message-ID: <27579291.59631336919783568.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 Dear Modellers, I sent this message a few days back too. What is the currently employed path to drive out of the reliable alignment mystery's vicious circle? Tell me a preliminary aspect of the script Salign_Multiple_Struc.py If multiple local folds are present in the computed alignment of this script for different templates, something like this, Template1>---AAAAAA---BBBBBBBB----* Template2>--APPPAAA---BCBBBB------* Template3>----AAA----BBBBBBBB-----* Template4>----AA-------BB---------* Elaborate the factors considered by MODELLER to put template2 close to the template1, and why template3 and 4 are kept away from template1 and closer to template2. Is it minimal RMSD of local template chunks, equal chunk lengths or something else. Give me the complete list of the considered factors considered in MODELLER for such a computation. Best Regards Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 4 Date: Tue, 15 May 2012 17:59:34 -0700 From: Xiao-Ping Zhang <xpzhang(a)ucdavis.edu> To: Modeller Caretaker <modeller-care(a)salilab.org> Cc: modeller_usage(a)salilab.org Subject: [modeller_usage] modeller.parallel.communicator.RemoteError Message-ID: <1337129974.5888.35.camel@localhost> Content-Type: text/plain; charset="ISO-8859-1" Hi, I got the following error when trying to run a old python script (see below) that worked very well before. A couple of days ago, I removed the Java came from the system (Fedora 13) and installed Java from java.com (jdk-7u4-linux-i586.rpm, jre-7u4-linux-i586.rpm) to fix a crash problem of Jalview. I wonder if the problem is related to the new Java or some other problems. Thank you. XP ############ my script ######################## # Homology modeling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class from modeller.parallel import * # Load the parallel class, #to use multiple processors # Use 5 CPUs in a parallel job on this machine j = job() # Cluster j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) j.append(local_slave()) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in env.io.hetatm = True # directories for input atom files env.io.atom_files_directory = ['.', '/usr/share/doc/modeller-9v8/examples'] a = automodel(env, alnfile = 'CC1295N.ali', # alignment filename knowns = ('1H6L', '1CVM1', '3AMR'), # codes of the templates sequence = 'CC1295N') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 20 # index of the last model # (determines how many models to calculate) a.use_parallel_job(j) a.make() # do the actual homology modeling #################### Errors ######################## Traceback (most recent call last): File "CC1295N_model.py", line 32, in ? a.make() # do the actual homologymodeling File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py", line 107, in make self.multiple_models(atmsel) File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py", line 208, in multiple_models self.parallel_multiple_models(atmsel) File "/usr/lib/modeller9.10/modlib/modeller/automodel/automodel.py", line 228, in parallel_multiple_models self.outputs.extend(job.run_all_tasks()) File "/usr/lib/modeller9.10/modlib/modeller/parallel/job.py", line 131, in run_all_tasks for task in self._finish_all_tasks(): File "/usr/lib/modeller9.10/modlib/modeller/parallel/job.py", line 164, in _finish_all_tasks task = self._process_event(obj, s) File "/usr/lib/modeller9.10/modlib/modeller/parallel/job.py", line 180, in _process_event task = obj.task_results() File "/usr/lib/modeller9.10/modlib/modeller/parallel/slave.py", line 61, in task_results r = self.get_data(allow_heartbeat=True) File "/usr/lib/modeller9.10/modlib/modeller/parallel/communicator.py", line 89, in get_data (cmdtype, obj) = self._recv() File "/usr/lib/modeller9.10/modlib/modeller/parallel/communicator.py", line 130, in _recv raise RemoteError(obj.exc, self) modeller.parallel.communicator.RemoteError: IndexError: user_form__E> Functional form 8195 out of range from <Slave on localhost> ##################################################### -----Original Message----- From: Modeller Caretaker <modeller-care(a)salilab.org> To: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] Error: Ran out of slaves to run tasks Date: Thu, 23 Feb 2012 10:54:11 -0800 On 2/21/12 9:39 AM, Modeller Caretaker wrote: > On 02/21/2012 08:55 AM, Xiao-Ping Zhang wrote: >> When I was refining loops for a model in parallel, I asked modeller to >> generate 9999 models. But modeller stopped at 1245 with the following >> error. The computer has six cores, modeller uses four of them. The other >> two cores were free. > ... >> ValueError: Ran out of slaves to run tasks > > This means exactly what it says: all of the slaves died, so it had > nowhere to run the loop model building tasks. Each slave generates its > own output file (look for files ending in .slave). Look in there to see > what the problem was with each slave. To conclude: it turned out that each slave was running out of memory. This is actually caused by a memory leak in Modeller that only affects parallel loopmodel runs. A patch is available to fix the problem at http://salilab.org/modeller/wiki/Patches Ben Webb, Modeller Caretaker ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 11, Issue 58 **********************************************

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sorry another one question
by Nandha Kumar 11 Aug '12

11 Aug '12

i am use (ex,cdh12 protein) modelling .using pdb_95.pir file ? -- nandhakumar

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