- modeller_usage - salilab.org

(OTCBB : DTMI) Special Investment Alert GQGT
by StockNews＠Telkom.net 15 Mar '02

15 Mar '02

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Re: Problems optimizing when BLK residues are present
by Cláudio Soares 08 Mar '02

08 Mar '02

Dear Modeller developers and users We have been using MODELLER for quite a while (since version 4.0) and we have now encountered two problems that I would like to share with you. These problems are of different nature and the first one is the most important one. I am referring to problems using MODELLER version 6.0 under i386 Linux. 1) We have proteins with non-standard co-factors, or simply co-factors that do not exist in the topology files (one example is FMN). When we derive the structure of the protein without the co-factors with standard optimisation procedures (such as refine 3), the structures come out all right with good Ramachandran plot and low values of the optimisation function. However, when we add these co-factors as BLK residues, the results are quite different, with much more Ramachandran violations and generally higher values of the objective function (which is not directly comparable between the two cases, but even so, the numbers are substantially different). This is an observation from a set of runs and its seems statistically significant. Another supporting evidence for a less good optimisation in these cases is the observation that loop regions (not defined by homology-derived restraints) are much similar between different generated models when BLK residues are included than when they are not. Do you think that this is a consequence of using BLK residues or a bug in the code? 2) When adding our own restraints to the homology derived restraints, the program crashes with segmentation fault. An example follows: -----------------------------------------------COMMAND FILE------------------- INCLUDE SET ATOM_FILES_DIRECTORY = './' SET ALNFILE = 'align2d.pir' SET KNOWNS = '1ar1' SET SEQUENCE = 'aa3' SET HETATM_IO = on SET WATER_IO = on SET HYDROGEN_IO = on SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' READ_RESTRAINTS FILE = 'my_rest.rsr', ADD_RESTRAINTS = on RETURN END_SUBROUTINE STOP ----------------------------------------------------------------------------- ------------------------------MY_REST.RSR------------------------------------ MODELLER5 VERSION: MODELLER FORMAT R 3 1 1 1 2 2 0 10 11 1.5000 0.0100 ----------------------------------------------------------------------------- This is a bond between two atoms, one belonging to a BLK residue and another one belonging to an haem. The same happens if any of the residues is a BLK residue. The same happens also when we use "USER FORMAT" instead. We tried to do this procedure in MODELLER 4.0 and it worked. It seems to be a bug then. Could you please help us with this? Thank you very much. Cláudio -------------------------------------------------------------------- Claudio M. Soares | ITQB | Av. da Republica, EAN |Phone:(351)214469610/214469100 Apartado 127 | Fax :(351)214411277 2781-901 Oeiras |email:claudio@itqb.unl.pt PORTUGAL |http://www.itqb.unl.pt/~claudio

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multiple domains
by Stefano Ciurli 08 Mar '02

08 Mar '02

I have the following question: I wish to model a series of homologous proteins (28 in total) for which I have the structure of the first and the 26th in order of sequence homology (ranging from ca. 55% to ca. 20%). The protein is made of two domains. The two available structures are quite similar except for the orientation of one domain with respect to the other (significantly off). What is the best approach to model sequences #2 to #25 and #27-#28??? Is there an accepted protocol in order to model multidomain proteins? I know that one of the biggest problems with modelling protein structures is encountered when you have more than one domain, that is, to model relative domain orientation. Is there a way out? How would you proceed using Modeller???

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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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restraints
by margot 08 Mar '02

08 Mar '02

Hi Modeller users/ support I am wondering if there is a systematic way to "soften" homology derived restraints in the modelling procedure. I want to do something in between homology modelling and loop modelling for some segments, for example reduce the template locally to backbone or Calpha only, and use softer distance restraints. Can anyone advise me of an efficient way of doing so? thanksalot margot

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Re: Modeller problem
by Bozidar Jerkovic 08 Mar '02

08 Mar '02

Gary, Unfortunately all questions regarding TRITON you will have to address to the author of the program, since we do not provide such support. For more information regarding MODELLER 6v1, please visit our web site at http://salilab.org/modeller Thank you, Bozidar On 8/3/02 4:18 AM, "Gary J Hunter" <ghun1(a)um.edu.mt> wrote: > Hi, I'm using triton 2.0beta with modeller 6a on an sgi Octane running irix > 6.5.6. I installed according to the instructions but get an error when trying > to run modeller. I've tried installing as root to a global system and as a > user installing to a personal system but I get the same error. I've tried the > example mutagenesis (and some of my own) and always get the following in the > OUTPUT STRUCTURE window: calculation finished with error My modeller key is... > (op.a.). Can you suggest what is wrong or how to proceed to get it working? > Thanks Gary -- > Gary J. Hunter > Associate Professor > Department of Physiology and Biochemistry phone : +356 32902917 / > 32902916 > Biomedical Sciences Building secretary: +356 316655 > University of Malta fax : > +356 310577 > Msida, MSD 06, MALTA email : > ghun1(a)um.edu.mt >

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Modeller for WIN
by Gianluca Croce 08 Mar '02

08 Mar '02

Hi modellers, I'm tring to use the new Modeller 6v2 on my windows 2000 but after set the keyword it don't run and I look this error from the DOS prompt: >C:\pgm\Modeller6v2\mod6v2\bin>modeller6v2.exe >forrtl: severe (29): file not found, unit 11, file >Image PC Routine Line Source >modeller6v2.exe 00630729 Unknown Unknown Unknown >modeller6v2.exe 00630587 Unknown Unknown Unknown >modeller6v2.exe 0062F764 Unknown Unknown Unknown >modeller6v2.exe 0062FB99 Unknown Unknown Unknown >modeller6v2.exe 00624E04 Unknown Unknown Unknown >modeller6v2.exe 0060728C Unknown Unknown Unknown >modeller6v2.exe 004CE573 Unknown Unknown Unknown >modeller6v2.exe 00657929 Unknown Unknown Unknown modeller6v2.exe 0064A144 Unknown Unknown Unknown KERNEL32.dll 77E97D08 Unknown Unknown Unknown ********************************** Dr. Gianluca Croce Ph.D. Student DISTA - University Amedeo Avogadro Corso Borsalino 54-15100 Alessandria-Italy Tel_office: +390131287414 Fax: +390131287416

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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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