- modeller_usage - salilab.org

New MODELLER 6v2 in a few weeks
by Bozidar 05 Mar '02

05 Mar '02

Hi everybody, Since lately there have been some reports on suspicious MODELLER 6v0/6v1 behavior and potential bugs from several people (Peng, Ramakrishna, Rute Fonseca, Claudio M. Soares, Thorsten Schweikardt, Reuter Nathalie, etc) I would like to let you know that we are working on these and some other issues and that we will have MODELLER 6v2 release in a few weeks that will address all these problems. In addition to that we will have MODELLER for Windows and IBM (either as a part of 6v2 or as a separate release on a later date). I know that some of you are eagerly awaiting this, but I implore you to be patient for a little bit more, so that we have good and stable version of MODELLER. Also I would like to use this opportunity to thank all of the people who have reported errors, problem and bugs with MODELLER. It's because of you that MODELLER gets better every day. Thanks, Bozidar

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Problem with Sequence_Search
by Thorsten Schweikardt 03 Mar '02

03 Mar '02

Hi Modellers, I am having a problem with the 'sequence_search' command in Modeller6, Modeller crashes after ~5 hours of searching with the following message (which is always the same, and looks similar to the one Francesco Musiani reported yesterday): projekte/limpo> mod6v1 search.top /home/thorsten/modeller6v1/bin/mod6v1: line 41: 1774 Killed $NICE ${EXECUTABLE} $STEERF >$LOGF I have already replaced the CHAINS files with the files from the new distribution, so the 1xnb-error does not occur anymore. As advised, I checked the stacksize, it is set to unlimited in the .cshrc-file, and remains set to this value before and after modeller's crash. I also tried different sequence-files, but there was no effect. Modeller is running on a Pentium3-800, SUSE-Linux 7.1, 640 MB RAM. Can anyone tell me what this error message means and how to solve this problem? Thanks in advance! Thorsten Schweikardt Molecular Biophysics University of Mainz Germany My files: search.top: ----------- SET OUTPUT_CONTROL = 1 1 1 1 0 SET FILE = 'limpo.pir' SEQUENCE_SEARCH ALIGN_CODES = 'limpo', DATA_FILE = ON limpo.pir: ---------- >P1;limpo sequence:limpo:::::::0.00:0.00 TLHDKQIRICHLFEQLSSATVIGDGDKHKHSDRLKNVGKLQPGAIFSCFHPDHLEEARHL YEVFWEAGDFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFI PSAAINEAFKKAHVRPEFDESPILVDVQDTGNILDPEYRLAYYREDVGINAHHWHWHLVY PSTWNPKYFGKKKDRKGELFYYMHQQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHL THVASGKYYSPRPDGLKLRDLGDIEISEMVRMRERILDSIHLGYVISEDGSHKTLDELHG TDILGALVESSYESVNHEYYGNLHNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIF YNWHRFIDNIFHEYKNTLKPYDHDVLNFPDIQVQDVTLHARVDNVVHTFMREQELELKHG INPGNARSIKARYYHLDHEPFSYAVNVQNNSASDKHATVRIFLAPKYDELGNEIKADELR RTAIELDKFKTDLHPGKNTVVRHSLDSSVTLSHQPTFEDLLHGVGLNEHKSEYCSCGWPS HLLVPKGNIKGMEYHLFVMLTDWDKDKVDGSESVACVDAVSYCGARDHKYPDKKPMGFPF DRPIHTEHISDFLTNNMFIKDIKIKFHE* logfile: -------- MODELLER 6v1, 17 Jan 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, Linux at2 2.4.0-4GB i686 Date and time of compilation : 01/24/2002 16:28:15 Job starting time (YY/MM/DD HH:MM:SS): 2002/03/01 11:51:45.460 TOP_________> 2 2 SET FILE = 'limpo.pir' TOP_________> 3 3 SEQUENCE_SEARCH ALIGN_CODES = 'limpo', DATA_FILE = ON openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/modlib//CHAINS_3.0_40_XN.cod openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/modlib//CHAINS_3.0_40_XN.cod openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/modlib//CHAINS_all.seq openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/modlib//CHAINS_all.seq openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/modlib//as1.sim.mat rdrrwgh_268_> Number of residue types: 20 openf5__224_> Open 11 OLD SEQUENTIAL limpo.pir seqsearc_> 1 limpo 1xnb 628 185 104 16.56 56.22 135506.30 _aln.pos 10 20 30 40 50 60 limpo TLHDKQIRICHLFEQLSSATVIGDGDKHKHSDRLKNVGKLQPGAIFSCFHPDHLEEARHLYEVFWEAG 1xnb ASTD-------YW-Q--NWT---DG------------G----G-I-----------------V----- _consrvd * * * ** * * * * _aln.p 70 80 90 100 110 120 130 limpo DFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFIPSAAINEAFKKAHVRP 1xnb --N-----A------VN-G--S-G------------GNY--------------S--VN--W------- _consrvd * * ** * * * * * _aln.pos 140 150 160 170 180 190 200 limpo EFDESPILVDVQDTGNILDPEYRLAYYREDVGINAHHWHWHLVYPSTWNPKYFGKKKDRKGELFYYMH 1xnb ----S-------NTGN-----F-V------VG-KG--W-------TTGSP--F-----RT--I-NY-N _consrvd * *** ** * * * * * * _aln.pos 210 220 230 240 250 260 270 limpo QQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHLTHVASGKYYSPRPDGLKLRDLGDIEISEMVRM 1xnb ----A---------GV--WAP-NG-N----GY---LT-L----Y------GWT-R-------SPLI-- _consrvd * * * * ** ** * * * * [....] The alignments stop with 1hv8.pdb, before the summary of the 1hv8-alignment is written.

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Fortran Runtime Error
by PENG 03 Mar '02

03 Mar '02

Hi, Modeller 6v0 is working fine on my Linux PC ( Redhat 7.1 ). But when I try Modeller 6v1, it says : ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... Could some one tell me how to correct this problem ? Thanks, Peng

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memory failure
by Francesco Musiani 28 Feb '02

28 Feb '02

Hi all, I'm using Modeller6 for the first time. I want to model a protein on a template but the program exit with this error in standard output: ---- /usr/local/bin/modeller6v1/bin/mod6v1: line 41: 10321 Segmentation fault (core dumped) $NICE ${EXECUTABLE} $STEERF >$LOGF ---- i'm using a Linux (RedHat) workstation with a Pentium4 and 512 MB RAM. regards, Francesco -- ------------------------------------------------------- Francesco Musiani --- PhD Student Web page: http://orion.agrsci.unibo.it/muso mail: musiani(a)sissa.it --- fmusiani(a)agrsci.unibo.it ------------------------------------------------------- Stelle già dal tramonto si contendono il cielo a frotte Luci meticolose nell'insegnarti la notte [F. DeAndre' - Il ritorno di Giuseppe]

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Silvana's question
by margot 28 Feb '02

28 Feb '02

Hi Silvana and everybody, my personal opinion is that Modeller is a bit intimidating for making first experiences with homology modelling. You could use the Expasy Swiss model server - you don't have to install a thing to play around a bit, and whenever you start wiorking on a project and know more about modelling, it may be time to get Modeller up and running. best wishes, a happy Modeller user (margot)

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** MODELLER Support ** Re: modeller
by Bozidar Jerkovic 27 Feb '02

27 Feb '02

Hi, Unfortunately MODELLER doesn't run under Windows yet. For other modeling programs please see the link below: http://salilab.org/bioinformatics_resources.shtml Best of luck, Bozidar > > Hi, > > That must be Windows 2000 > > regards, > Silvana > > > ----- Original Message ----- > From: Bozidar Jerkovic <bozidar(a)salilab.org> > Date: Thursday, February 28, 2002 12:35 pm > Subject: Re: modeller > >> >> Hi, >> >> You haven't specified what OS is your PC running under. MODELLER >> runs on PCs >> with Linux OS. >> >> Thanks, >> Bozidar >> >> >>> Hi, >>> >>> My name is Silvana Sekuloski and I am doing PhD in science at >>> University of Technology, Sydney. At the moment I am very >> interested to >>> learn a little bit about Protein modelling. Modeller was a >> program that >>> has been recomended to me,but as far as I know about computers >> it seems >>> that I can not install it on my PC computer. I was just >> wondering if >>> you could tell me if there is another version or any other >> program for >>> protein modelling that could run on a PC (and easy to learn to work >>> with it) >>> >>> Regards >>> >>> Silvana Sekuloski >>> >>> >>> >>> CRICOS Number: 00099F >>> >>> DISCLAIMER >>> >> > =====================================================================> > This email message and any accompanying attachments may contain >>> confidential information. If you are not the intended >> recipient, do not >>> read, use, disseminate, distribute or copy this message or >> attachments.> If you have received this message in error, please >> notify the sender >>> immediately and delete this message. Any views expressed in this >> message> are those of the individual sender, except where the >> sender expressly, >>> and with authority, states them to be the views the University of >>> Technology Sydney. Before opening any attachments, please check >> them for >>> viruses and defects. >>> >> > =====================================================================> >> >> >> > > > > CRICOS Number: 00099F > > DISCLAIMER > ===================================================================== > This email message and any accompanying attachments may contain > confidential information. If you are not the intended recipient, do not > read, use, disseminate, distribute or copy this message or attachments. > If you have received this message in error, please notify the sender > immediately and delete this message. Any views expressed in this message > are those of the individual sender, except where the sender expressly, > and with authority, states them to be the views the University of > Technology Sydney. Before opening any attachments, please check them for > viruses and defects. > ===================================================================== >

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Re: modeller
by Bozidar Jerkovic 27 Feb '02

27 Feb '02

Hi, You haven't specified what OS is your PC running under. MODELLER runs on PCs with Linux OS. Thanks, Bozidar > Hi, > > My name is Silvana Sekuloski and I am doing PhD in science at > University of Technology, Sydney. At the moment I am very interested to > learn a little bit about Protein modelling. Modeller was a program that > has been recomended to me,but as far as I know about computers it seems > that I can not install it on my PC computer. I was just wondering if > you could tell me if there is another version or any other program for > protein modelling that could run on a PC (and easy to learn to work > with it) > > Regards > > Silvana Sekuloski > > > > CRICOS Number: 00099F > > DISCLAIMER > ===================================================================== > This email message and any accompanying attachments may contain > confidential information. If you are not the intended recipient, do not > read, use, disseminate, distribute or copy this message or attachments. > If you have received this message in error, please notify the sender > immediately and delete this message. Any views expressed in this message > are those of the individual sender, except where the sender expressly, > and with authority, states them to be the views the University of > Technology Sydney. Before opening any attachments, please check them for > viruses and defects. > ===================================================================== >

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starting modeller: what's wrong?
by Ari M. Siqueira 27 Feb '02

27 Feb '02

Hi, I have just installed Modeller 6.0v1 on my P-III, Conectiva Linux (RH-like), under /usr/local/bin/modeller6v1/ My .bashrc reads: # .bashrc # User specific aliases and functions # Source global definitions if [ -f /etc/bashrc ]; then . /etc/bashrc fi ### begin MODELLER6v1 ###################################################### MODINSTALL6v1=/usr/local/bin/modeller6v1 EXECUTABLE_TYPE6v1=i386-absoft LIBS_LIB6v1=$MODINSTALL6v1/modlib/libs.lib KEY_MODELLER6v1=XXX mod=mod6v1 export MODINSTALL6v1 EXECUTABLE_TYPE6v1 LIBS_LIB6v1 KEY_MODELLER6v1 mod PATH=$PATH:$MODINSTALL6v1/bin ulimit -S -s unlimited ### end MODELLER6v1 ######################################################## Attempts to run Modeller: 1. When I try 'mod model-default'I get 'bash: mod: command not found' 2. When I try '/usr/local/bin/modeller6v1/bin/mod6v1 model-default'I get 'STOP' 3. When I try '/usr/local/bin/modeller6v1/bin/mod6v1_i386-absoft model-default' I get something more interesting: MODELLER 6v1, 17 Jan 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux home.localdomain 2.2.17-14cl i686 Date and time of compilation : 01/24/2002 16:28:15 Job starting time (YY/MM/DD HH:MM:SS): 2002/02/27 16:50:50.084 fullfn__230E> File not found: model-default Directories: :${MODINSTALL6v1}/bin/ Extensions : .top: Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139.608 2.089 Starting time : 2002/02/27 16:50:50.084 Closing time : 2002/02/27 16:50:51.154 Total CPU time [seconds] : 1.03 STOP I trust someone can help me. Yours thankfully, Ari M. Siqueira, PhD Associate Professor of Biochemistry ICB - UFMG Brazil

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basic question?
by Michael Buck 26 Feb '02

26 Feb '02

Can you directly compare the objective function between two models created using different templates? If not where can you find the Fsymm term used in the objective function? Secondly, are Fstatic and Fdynamic from the objective function comparable between two models using different templates? Thanks for your help, Michael ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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modelling of small peptide
by Violet Chang 26 Feb '02

26 Feb '02

Hi Modellers, I understand that it's not a good idea using Modeller to model the very small peptdie(Here I tried to model the pentapeptide). And I've read the reply posted by Fiser about forcing modeling to deal only with sidechains and retain the same backbone conformation. However, I'd like to know if it's possible to achive the same goal by setting the "SET DEVIATION = 0.0'. I have built different models by different .top files. The first one is with 'SET DEVIATION= 0.0'. And the second one, in addition to 'SET DEVIATION= 5.0', is included a subroutine called 'select_atoms'. Then the rms among models and templates are around 0.435-1.774. Can you please help me explain the results? I don't know how much meanings my models have. Thanks very much. Best regards, Violet Violet(Chiung-wen) Chang, Ph.D. Student Department of Physiology and Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine One Gustave L. Levy Place, Box 1022, New York, NY 10029 phone: (212) 241 1611

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