- modeller_usage - salilab.org

Creating an oligonucleotide sequence.
by Andy Torelli 18 Jul '03

18 Jul '03

Dear MODELLER Users, I would like to model a short nucleotide sequence as a substrate for an enzyme. In the top_heav.lib file, I notice that the listing for URA (a uridine mono-phosphate molecule) has bond angle entries that include '+' and '-' prefixes on some of the atoms (referring to atoms in molecules adjacent in a chain sequence). I was under the impression that these entries were enough to form a connected sequence of molecules (in this case, an oligonucleotide). In my alignment file, I have two of these URA molecules situated next to each other (separated from the amino acids of my enzyme by a chain break character '/'), but in the final model, they do not appear to be bonded to each other. As a test, I substituted two amino acids for the two URA molecules and noticed that in the final model, they were not joined by a bond either. Since the amino acids of my enzyme were all clearly bonded to each other, this result made me wonder if MODELLER was not recognizing my two substrate molecules as being members of a chain themselves (albeit two subunits long). - Do I need to, or can I, explicitly define these two (nucleotide) molecules as being members of a chain such that MODELLER will create a phosphodiester bond between them? - Is it possible that they would normally be bonded, but during the simulation, the molecules are being "torn apart"? - My other option appears to be to impose a "special_patches" restraint (that I would have to add to the top_heav.lib file) to explicitly join them. However, seeing that the URA residue listing already appears to be set up for nucleotide chains, this seems like it would be unnecessary. Thanks for your time, Sincerely, -Andy Torelli Ph.D. Student University of Rochester, Department of Biochemistry and Biophysics

1 0

mod6v2 still doesn't work on FreeBSD
by Peter C. Lai 17 Jul '03

17 Jul '03

Hi everyone, I asked about using modeller 6v2 last year on FreeBSD which did not work. After redownloading the latest build from Bozidar, running mod6v2-i386-absoft on FreeBSD results in computation of stuff but no files are output, and around the time the modelling should be complete, it core dumps with Bad system call. This happens with running mod6v2-i386-nag also. I know Nag has a port of the F95 compiler for FreeBSD; not sure if you guys have a copy or not. Currently, I'm using modeller on my windows machine, but it would really be nice to run it on my FreeBSD workstation. In the previous year I have been running it on SGI, but currently the SGI is being used for dynamics. My FreeBSD setup is 4.8-STABLE, with linux_base-7.1 (linux emulation ABI) installed. Wondering if you had any suggestions. Thanks. pete -- Peter C. Lai University of Connecticut Dept. of Molecular and Cell Biology Yale University School of Medicine SenseLab | Research Assistant http://cowbert.2y.net/

1 0

FW: modeller
by Modeller Care 17 Jul '03

17 Jul '03

------ Forwarded Message From: "Mehriar Amininasab" <amininasab(a)ibb.ut.ac.ir> Date: Thu, 17 Jul 2003 17:39:12 +0430 To: bozidar(a)salilab.org Subject: modeller Dear Dr. Bozidar I have a 3D structure of a complex between a protein and its peptidic ligand. I would like to change some amino acids of the protein in complex or replace the ligand with another one or do them simoultaneously and model the complex. Would you please inform me to do this and how to make .ali and .top for this task. Thanks in advance, Mehriar Amininasab Inst Biochem Biophys, po box 13145-1384, Tehran Univ, Tehran-IRAN ------ End of Forwarded Message

1 0

Re: help running run_tops1
by Modeller Care 17 Jul '03

17 Jul '03

It was a little early this morning when I forwarded Feng's message, I should have answered it right then. The run_tops1 file is not a modeller top file. It is a script that runs a number of modeller jobs. This is the content: run_tops1: #!/bin/sh mod6v2 initial mod6v2 model-default mod6v2 model-segment mod6v2 model-fast mod6v2 model-loop # procheck 1fdx.B999901 2.0 mod6v2 compare It is a unix shell script. In a unix environment, you would execute it like this: cd whereever/examples/tutorial-model ./run_tops1 all those top files (initial.top, model-default.top, etc.) are in this directory. For windows, you should remove the first line of the script and the procheck line (commented out in the unix script), and rename it run_tops1.bat. Then you should change mod6v2 to mod, execute the modenv.bat file to set the environment, and execute it as run_tops1 from the tutorial-model directory. Hope this solves your problem. Best regards, Ursula ---------------------------------------------- Ursula Pieper, Ph.D. Laboratory of Andrej Sali Mission Bay Genentech Hall 600 16th Street, Suite N474P University of California, San Francisco San Francisco, CA 94143-2240 email: ursula(a)salilab.org phone: 415-514-4233 On 7/17/03 8:33, "Rolando Pajon Feyt" <rolando.pajon(a)cigb.edu.cu> wrote: > Dear all: > > I have de very same problem (see message below). Can anyone help us? > > Regards > > rolando > > Dr. Rolando Pajón Feyt > > Head of Meningococcal Reseach Department > > Vaccine Division > > Centro de Ingeniería Genética y Biotecnología > > Ave 31 e/ 158 y 190, Cubanacán, Playa. > > PO BOX 6162 > > Ciudad Habana > > CP 10600 > > Cuba > > Volverán > > > > > -----Original Message----- > From: Modeller Care [mailto:modeller-care@salilab.org] > Sent: Thursday, July 17, 2003 10:03 AM > To: modeller_usage(a)salilab.org > Cc: Feng Cui > Subject: FW: help > > > > > Message forwarded by list owner > > ------ Forwarded Message > From: Feng Cui <fengcui(a)iastate.edu> > Date: Wed, 16 Jul 2003 18:05:51 -0500 (CDT) > To: modeller-care(a)salilab.org > Subject: help > > > Sir, > > i downloaded the Modeller 6v2 on my laptop (windows xp). i modified the > mod.bat and modenv.bat based on the Readme file. i tried to run a test case > upon the window command prompt. but the program seems not to be ale to > recognize the MOD6V2 command. the error message is following: > > C:\Downloads\modeller6v2\bin>mod.bat ..\examples\tutorial-model\run_tops1 > > C:\Downloads\modeller6v2\bin>set MODINSTALL6v2=c:\Downloads\modeller6v2 > > C:\Downloads\modeller6v2\bin>set KEY_MODELLER6v2=XXX > > C:\Downloads\modeller6v2\bin>set LIBS_LIB6v2=c:\Downloads\modeller6v2 > \modlib\lib > s.lib > > C:\Downloads\modeller6v2\bin>set EXECUTABLE_TYPE6v2=i386-windf > > C:\Downloads\modeller6v2\bin>set PATH=c:\Downloads\modeller6v2 > \bin;C:\Perl\bin\; > C:\texmf\miktex\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32 > \Wbem;C:\P > rogram Files\Common Files\Adaptec Shared\System;c:\matlab6p5 > \bin\win32;C:\KERB;C > :\j2sdk1.4.1_02\bin;c:\Downloads\modeller6v2\bin;c:\Downloads\modeller6v2 > \bin;c: > \Downloads\modeller6v2\bin;c:\Downloads\modeller6v2 > \bin;c:\Downloads\modeller6v2 > \bin;c:\Downloads\modeller6v2\bin > > C:\Downloads\modeller6v2\bin>c:\Downloads\modeller6v2 > \bin\modeller6v2 ..\example > s\tutorial-model\run_tops1 > > MODELLER 6v2, 17 Feb 2002 > > PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS > > > Copyright(c) 1989-2002 Andrej Sali > All Rights Reserved > > Written by A. Sali > with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, > B. Jerkovic, A. Badretdinov, F. Melo, > J.P. Overington & E. Feyfant > Rockefeller University, New York, USA > Harvard University, Cambridge, USA > Imperial Cancer Research Fund, London, UK > Birkbeck College, University of London, London, UK > > > Kind, OS, HostName, Kernel, Processor: 4, Windows_NT WUGRADS x86 Family 15 > Model > 2 Stepping 7, Genuine > Date and time of compilation : Jul 09 2002 16:21:30 > Job starting time (YY/MM/DD HH:MM:SS): 2003/07/16 17:53:12.039 > > rdactio_534E> Command not recognized: MOD6V2 INITIAL > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > Dynamically allocated memory at finish [B,kB,MB]: 2190959 > 2139. > 608 2.089 > Starting time : 2003/07/16 > 17:53:12. > 039 > Closing time : 2003/07/16 > 17:53:13. > 200 > Total CPU time [seconds] : 0.91 > > C:\Downloads\modeller6v2\bin> > > please let me know what i should do. thanks. > > Feng Cui > > > > > > > > ------ End of Forwarded Message > > > >

1 0

FW: help
by Modeller Care 17 Jul '03

17 Jul '03

Message forwarded by list owner ------ Forwarded Message From: Feng Cui <fengcui(a)iastate.edu> Date: Wed, 16 Jul 2003 18:05:51 -0500 (CDT) To: modeller-care(a)salilab.org Subject: help Sir, i downloaded the Modeller 6v2 on my laptop (windows xp). i modified the mod.bat and modenv.bat based on the Readme file. i tried to run a test case upon the window command prompt. but the program seems not to be ale to recognize the MOD6V2 command. the error message is following: C:\Downloads\modeller6v2\bin>mod.bat ..\examples\tutorial-model\run_tops1 C:\Downloads\modeller6v2\bin>set MODINSTALL6v2=c:\Downloads\modeller6v2 C:\Downloads\modeller6v2\bin>set KEY_MODELLER6v2=XXX C:\Downloads\modeller6v2\bin>set LIBS_LIB6v2=c:\Downloads\modeller6v2 \modlib\lib s.lib C:\Downloads\modeller6v2\bin>set EXECUTABLE_TYPE6v2=i386-windf C:\Downloads\modeller6v2\bin>set PATH=c:\Downloads\modeller6v2 \bin;C:\Perl\bin\; C:\texmf\miktex\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32 \Wbem;C:\P rogram Files\Common Files\Adaptec Shared\System;c:\matlab6p5 \bin\win32;C:\KERB;C :\j2sdk1.4.1_02\bin;c:\Downloads\modeller6v2\bin;c:\Downloads\modeller6v2 \bin;c: \Downloads\modeller6v2\bin;c:\Downloads\modeller6v2 \bin;c:\Downloads\modeller6v2 \bin;c:\Downloads\modeller6v2\bin C:\Downloads\modeller6v2\bin>c:\Downloads\modeller6v2 \bin\modeller6v2 ..\example s\tutorial-model\run_tops1 MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Windows_NT WUGRADS x86 Family 15 Model 2 Stepping 7, Genuine Date and time of compilation : Jul 09 2002 16:21:30 Job starting time (YY/MM/DD HH:MM:SS): 2003/07/16 17:53:12.039 rdactio_534E> Command not recognized: MOD6V2 INITIAL recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139. 608 2.089 Starting time : 2003/07/16 17:53:12. 039 Closing time : 2003/07/16 17:53:13. 200 Total CPU time [seconds] : 0.91 C:\Downloads\modeller6v2\bin> please let me know what i should do. thanks. Feng Cui ------ End of Forwarded Message

1 0

Re: Using a model file as one of the templates (fwd)
by sasson iris 11 Jul '03

11 Jul '03

Hi Margot, Thank you for your reply. I know i may use multiple alignment. My problem concerns using models that were not inferred from alignments. That is, in addition to a multiple alignment i may have, i want modeller to use models of the query sequence. for example: if the sequence to model is : ATCE i have a 3d file of it (pdb format): ATOM .... CA ... ALA ... x_cord y_cord z_zord ATOM .... CA ... THR ... x_cord y_cord z_zord ATOM .... CA ... CYS ... x_cord y_cord z_zord ATOM .... CA ... GLU ... x_cord y_cord z_zord (of course, my sequence is longer). I have no alignment of this, since the model contains the same sequence as the query (because it is a model of the query). I have read the manual, modeller gets alignments as input, not models. I want modeller to use the models i have and the multiple alignment i have, in order to generate a new model. I do not know how to do this. I will be happy to check any suggestion you may have. Thanks, Iris. On Fri, 11 Jul 2003, Margot Ernst wrote: > Hi Iris, > in principle you can use any model as template by adding it to the list of > "KNOWNS" in your topscript. > Modeller can use several templates at once. I recommend you look through the > appropriate examples in the documentation. In the tutorial chapter is a > topscript showing you how to model on 4 templates. They need to be present in > the alignment, of course and their pdb files have to be in the appropriate > atoms file directory. > good luck > margot > > On Thursday 10 July 2003 16:03, sasson iris wrote: > > Hi, > > > > I send this question again because i got no reply. > > > > I want to create a model using modeller from a group of alignmnets and > > models. Since modeller (if i understand correctly) uses only alignments > > and no models (pdb format), i would like to create alignmnets from the > > models i have, and give the alignment as one of the alignmnets in the > > multiple alignmnet given as input to modeller. However, i have no idea how > > to do this since i do not know what modeller actually does. > > An alignment that may be created from a model i already have > > > > is of identical sequences of query and template like this: > > >P1;str > > > > structure : str : : : : : : : : > > EFSVCGGRLIKLSHNSNSTKTSMNVNIYLPKHYYAQDFPRNKRIPTVFYLSGLTCTPDNASEKAFWQFQADKYGF > >AIVFP EHLKPELLLEAVKATSWQDYVEIKKVHGFDHSYYFVSTFVPEHAEFHARNLGLI* > > > > >P1;query > > > > sequence : query : : : : : : : : > > EFSVCGGRLIKLSHNSNSTKTSMNVNIYLPKHYYAQDFPRNKRIPTVFYLSGLTCTPDNASEKAFWQFQADKYGF > >AIVFP EHLKPELLLEAVKATSWQDYVEIKKVHGFDHSYYFVSTFVPEHAEFHARNLGLI* > > > > and i have the model which is the str.pdb file. > > I do not want modeller to put higher weight to this alignment than to the > > others (which are to real templates). The sequence identity may yield this > > result. How can i solve this? > > Or if i ask it differently, what weight does modeller give to such > > alignmnets? How can i change the sequence similarity to yield the required > > result? > > I will be happy to check any suggestion you may have. > > > > Thanks, > > Iris. > > > > > > > > ---------- Forwarded message ---------- > > Date: Sun, 6 Jul 2003 15:37:31 +0300 (IDT) > > From: sasson iris <sassonir(a)cs.bgu.ac.il> > > To: Modeller Care <modeller-care(a)salilab.org> > > Cc: modeller_usage(a)salilab.org > > Subject: Using a model file as one of the templates > > > > > > Hi, > > > > I want to use models as well as templates to build a new model using > > modeller. That is, I have a few models that were not created by using an > > alignment and some alignments. > > How can i make modeller use all of which to build a new model? > > > > Thanks, > > Iris. > >

1 0

complex
by Thijs Beuming 10 Jul '03

10 Jul '03

Dear all, Can anyone tell me if (and how) it is possible to model a protein complex in Modeller? How do I tell Modeller that the two proteins are not connected? Thanks, Thijs Beuming

2 1

Using a model file as one of the templates (fwd)
by sasson iris 10 Jul '03

10 Jul '03

Hi, I send this question again because i got no reply. I want to create a model using modeller from a group of alignmnets and models. Since modeller (if i understand correctly) uses only alignments and no models (pdb format), i would like to create alignmnets from the models i have, and give the alignment as one of the alignmnets in the multiple alignmnet given as input to modeller. However, i have no idea how to do this since i do not know what modeller actually does. An alignment that may be created from a model i already have is of identical sequences of query and template like this: >P1;str structure : str : : : : : : : : EFSVCGGRLIKLSHNSNSTKTSMNVNIYLPKHYYAQDFPRNKRIPTVFYLSGLTCTPDNASEKAFWQFQADKYGFAIVFP EHLKPELLLEAVKATSWQDYVEIKKVHGFDHSYYFVSTFVPEHAEFHARNLGLI* >P1;query sequence : query : : : : : : : : EFSVCGGRLIKLSHNSNSTKTSMNVNIYLPKHYYAQDFPRNKRIPTVFYLSGLTCTPDNASEKAFWQFQADKYGFAIVFP EHLKPELLLEAVKATSWQDYVEIKKVHGFDHSYYFVSTFVPEHAEFHARNLGLI* and i have the model which is the str.pdb file. I do not want modeller to put higher weight to this alignment than to the others (which are to real templates). The sequence identity may yield this result. How can i solve this? Or if i ask it differently, what weight does modeller give to such alignmnets? How can i change the sequence similarity to yield the required result? I will be happy to check any suggestion you may have. Thanks, Iris. ---------- Forwarded message ---------- Date: Sun, 6 Jul 2003 15:37:31 +0300 (IDT) From: sasson iris <sassonir(a)cs.bgu.ac.il> To: Modeller Care <modeller-care(a)salilab.org> Cc: modeller_usage(a)salilab.org Subject: Using a model file as one of the templates Hi, I want to use models as well as templates to build a new model using modeller. That is, I have a few models that were not created by using an alignment and some alignments. How can i make modeller use all of which to build a new model? Thanks, Iris.

1 0

Re: B-factor column
by Margot Ernst 10 Jul '03

10 Jul '03

Hi Jonathan, and thank you so much for taking the time to explain. This is as I suspected, now I would like to find out more on how it is computed: Do restraint violations enter this figure? Which "information" is there to support a piece of alignment in a remote homologue, do alignment scores enter, how is it computed for insertions, etc? Is there any place where I can read up on how this figure is computed in Modeller? Unlike in crystallography, there is no "experimental" evidence for any of my modeled atomic positions, which is why the analogy makes sense but leaves me clueless on which information enters the "modeling confidence factor". If there is any way for me to do the homework myself by reading up I would happily pick up anything that is suggested. margot On Wednesday 09 July 2003 18:42, you wrote: > Hi, > > The B-factor also known as the confidence factor in > homology modeling, is practically based on the amount > of information that supports each region of the model. > > It is a measure of uncertainty so, high value implies > low confidence about a specific part of the model. (In > crystallography, high B-factor imply uncertainty in > assignment of atom positions). > > Note that large B factors are assigned to atoms or > residues built without a template, including loops, > reflecting the lack of template support for those > parts of the model. > > cheers, > ./jonathan > > > > --- Margot Ernst <margot.ernst(a)univie.ac.at> skrev: > > Hi Modeller community, > > > unfortunately I have not received any answer, so I > > will repeat my question as > > I REALLY would like to know: What is the value in > > the B-factur column of the > > structure files Modeller generates? > > Thanks for your help, > > margot > > -- > > ----------------------------------------------------------------- > > > | Dr. Margot Ernst > > | > > | Abteilung Prof. Sieghart > > | > > | Institut f. Hirnforschung/brainresearch institute > > | > > | Spitalgasse 4 > > | > > | A-1090 WIEN VIENNA, Austria > > | > > | margot.ernst(a)univie.ac.at > > | > > | visit http://www.univie.ac.at/brainresearch > > ----------------------------------------------------------------- > > > the bottom line to brainresearch: > > If the brain was so simple that you could understand > > it, > > you would be so simple that you couldn't. (unknown) > > --------------------------------------------------------- > > > "Research: If it worked the first time, > > they would just call it 'search'." -Roy Garcia > > -------------------------------------------------------- > > ----------------------------------------------------------------- > > > > _____________________________________________________ > Gå före i kön och få din sajt värderad på nolltid med Yahoo! Express > Se mer på: http://se.docs.yahoo.com/info/express/help/index.html -- ----------------------------------------------------------------- | Dr. Margot Ernst | Abteilung Prof. Sieghart | Institut f. Hirnforschung/brainresearch institute | Spitalgasse 4 | A-1090 WIEN VIENNA, Austria | margot.ernst(a)univie.ac.at | visit http://www.univie.ac.at/brainresearch ----------------------------------------------------------------- the bottom line to brainresearch: If the brain was so simple that you could understand it, you would be so simple that you couldn't. (unknown) --------------------------------------------------------- "Research: If it worked the first time, they would just call it 'search'." -Roy Garcia -------------------------------------------------------- -----------------------------------------------------------------

1 0

AW: difference between FASTA and PDB
by Thorsten Schweikardt 07 Jul '03

07 Jul '03

Hello YeBin, Modeller states that you have more aminoacids in the alignment than in the pdb-file (353/352), and if you compare the fasta-sequence and the pdb-file you will find a lysine (K) at the C-terminus that is not present in the pdb-file. Delete the K from your alignment or change it to a "-" and Modeller should work fine. Remember that there might no be all aminoacids present in a pdb-file for structural reasons: loops at the surface may be highly mobile, and can therefore often not be solved by crystallography, and that means you will have a gap in the structure. Before modelling, check the sequence. You can use DeepView to write out the aminoacids present in the pdb-file by loading the protein and then saving the sequence in FASTA-format. Best wishes, Thorsten

1 0