- modeller_usage - salilab.org

MODELLER web page problem with debbuger turned on in MS Internet Explorer
by Bozidar Jerkovic 07 Mar '02

07 Mar '02

Hi, There have been some problems with Java script that controls that table and it is fixed now. Please try again. In case you still can not get there please go directly to the download page at: http://salilab.org/modeller/current_version.shtml Thanks, Bozidar -----Original Message----- From: sompallae Ramakrishna Rao [mailto:ramakrishnaraos@yahoo.co.in] Sent: Saturday, March 02, 2002 1:11 AM To: Bozidar Jerkovic Subject: Re: reg: trouble shooting modeller Installation Dear Sir, Thankyou very much for your reply. well the problem i am facing with modeller6v is. I dont have my linux operating system configured with net so i have to download the things on my windows operating system and write it on to a CD and copy it onto Linux. when i visit modeller home page on the left side there is a table rather a list, where in one cell has hyperlink for Download and installation if i move the cursor over any of those cells it throughs an error popup messagebox, saying their is a "Runtime error occured" do you wish to debug? Line :215/208 etc error : object expected i am unable to proceed further and download. modeller4 i have downloaded earlier (april 2001), and iam using it now. what should i do to proceed further, ishall be greatful to u for all ur help. thank you very much. with regards ramakrishna --- Bozidar Jerkovic <bozidar(a)salilab.org> wrote: > > Hi, > > Please download MODELLER 6v1. We don't support > anymore MODELLER 4. It is not > clear from your email what kind of problem are you > having downloading > MODELLER 6v1. > > Thanks, > Bozidar ________________________________________________________________________ Looking for a job? Visit Yahoo! India Careers Visit http://in.careers.yahoo.com

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(OTCBB : LMGR) Paves the way in the Field of Optics D
by StockAlerts＠Telkom.net 07 Mar '02

07 Mar '02

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restraints
by margot 07 Mar '02

07 Mar '02

Hi Modeller Users and Support if this is a resend, please forgive me - I tried to send this yesterday but it looked like it bounced. The question is: Is there any efficient, systematic way to "soften" or "loosen" homology derived restraints? What I have in mind is to model some (SCR) segments with regular homology derived restraints and others (SVR) with, say Calpha or backbone from the template only, less stringent geometric homology derived restraints and more thorough refinement (i.e. the halfway point between regular homology modelling and loop modelling). Short of editing the restraints by hand - any efficinet way of doing so? thanksalot, margot

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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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