February 2002 - modeller_usage

Strange Error
by Michael Buck 08 Mar '02

08 Mar '02

I am having the following error message: rdpir___270E> Error reading/processing file: tempalign recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I can fix the problem by open my alignment file "tempalign" and resaving it with a unix text editor like pico, even if I don't change any thing in the file it will then work fine. Does anybody know what is causing this error? I use perl scripts to write my alignment files and can't find what is causing the error. Is there a hidden character I can't see? Thanks, Michael Buck ************************************************ 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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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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Hello Sir
by deepa thangavelu 25 Feb '02

25 Feb '02

Hello Sir, I'm doing project by using modeller. I couldn't install the modeller page.It is showing error,when i click the download&installation option. So,i kindly request you to correct this page as early as possible. Thanking You Your's Truely, Deepa. ________________________________________________________________________ Looking for a job? Visit Yahoo! India Careers Visit http://in.careers.yahoo.com

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Re: starting problem (fwd)
by Boojala Reddy 20 Feb '02

20 Feb '02

You make similar file like ali using your sequence and a homologus structure(s) and follow the steps as explained in the modeller manual. There is a modeller users form. You please mail your quary to them. I am copieing this e-mail to them. Best .../BVB | Boojala V. B. Reddy Ph. D. | | Assistant Research Scientist | | University of California, San Diego Fax: (858)-822-0873 | | San Diego Supercomputer Center(SDSC) Voice: (858)-822-0860 | | Chemistry Research Bulding (CRB-166) | | 9500 Gilman Drive, e-mail: breddy(a)sdsc.edu | | La Jolla, CA 92093-0537 http://www.sdsc.edu/~breddy | ---------- Forwarded message ---------- Date: Mon, 18 Feb 2002 14:23:15 +0530 (GMT+5:30) From: Gowthaman R <gowtham(a)icgeb.res.in> To: Boojala Reddy <breddy(a)sdsc.edu> Subject: Re: starting problem hi reddy this is gowtham a graduate student doing phd at ICGEB New delhi. im planning to do some 3d predictions using the modeller i installed adn the tutorial is running fine. now i would like to use some malarial protiens but i donot kow how to get the input files like .ali files ...... im unable to start my work. can u help me out in this regard.........and it is bit urgent. i would be thankful to u verymuch waiting for ur reply regards gowtham

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