- modeller_usage - salilab.org

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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error message how to sol
by Nandha Kumar 11 Aug '12

11 Aug '12

error openf______E> Cannot open file qseq1-tseq1.ali: No such file or directory -- nandhakumar

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how to download pdb_95.pir&bin file
by Nandha Kumar 11 Aug '12

11 Aug '12

questions 1.why use pdb _95.pir&bin? 2.another modelling using pdb_95 .pir&bin? -- nandhakumar

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i am using windows 8 os
by Nandha Kumar 10 Aug '12

10 Aug '12

[' import site' failed; use -v for traceback cannot open logfile model-default.py: permission denied] please help me -- nandhakumar

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(no subject)
by Nandha Kumar 10 Aug '12

10 Aug '12

[' import site' failed; use -v for traceback cannot open logfile model-default.py: permission denied] -- nandhakumar

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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 83
by Ashish Runthala 09 Aug '12

09 Aug '12

Dear James, You search for Salign_*.py scripts in MODELLER and then you can integrate both the templates. However, you need to include both the template to later curate the alignment file as per your fusion consideration requirement. Regards 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, 8 August, 2012 18:57:12 GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 83 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: struggling to make structure predictions (Modeller Caretaker) 2. Template PDB files (Nanda Pandey) 3. Re: Template PDB files (Modeller Caretaker) 4. Modelling of Chimeric protein (James Starlight) ---------------------------------------------------------------------- Message: 1 Date: Mon, 06 Aug 2012 18:22:09 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: "Adhikari, Badri (MU-Student)" <bap54(a)mail.missouri.edu> Cc: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] struggling to make structure predictions Message-ID: <50206DC1.10905(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 8/6/12 2:24 PM, Adhikari, Badri (MU-Student) wrote: > I am struggling to write a python program that takes protein sequence as > input and produces some conformations as the output (with no any other > input data). The scripts you've attached are IMP scripts. This is the Modeller mailing list. You'd probably have more luck on the IMP mailing list. 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: Tue, 7 Aug 2012 17:38:21 +0530 From: Nanda Pandey <pnanda1780(a)gmail.com> To: modeller_usage(a)salilab.org Subject: [modeller_usage] Template PDB files Message-ID: <CAPR-BHD352XAOK_w-k2aia7wyN+N8_z5q=vS_NhxYVVPDzTsOQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I am very new to modeller so a small query, Please let me know how do I compare the template sequences using compare script. Do I need to download individual template files from PDB or Is there any other possible way. Also, whta should be done in case I have too many template sequences with same e -value (e.g. 0 e -value) should i download all of them?? Thanks and Regards.

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Modelling of Chimeric protein
by James Starlight 08 Aug '12

08 Aug '12

Dear Modeller's users! I want to model chimeric protein which consist of two fussed proteins ( tail to head fussion C to N termi). It's important that both of that proteins have known spatial structures which could be used as the templates. In the input I can define merged sequences of my proteins as one entry. Is there any way to use both of the templates to guide such modelling ? In the input option I've found only possibility to use one template. What extra additions should I provide for better modelling of the fussed protein? Thanks for help Gleb

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Template PDB files
by Nanda Pandey 07 Aug '12

07 Aug '12

Hi, I am very new to modeller so a small query, Please let me know how do I compare the template sequences using compare script. Do I need to download individual template files from PDB or Is there any other possible way. Also, whta should be done in case I have too many template sequences with same e -value (e.g. 0 e -value) should i download all of them?? Thanks and Regards.

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