modeller_usage

modeller_usage@salilab.org

5 participants
3147 discussions

Re: Modeller on linux
by Lutfullah Kakakhel 18 Oct '98

18 Oct '98

Hello, I have discovered that 'i386-linux' is set in my linux kernel and it would require re-compilation of kernel to change it to 'i486-linux' or whatever and that it also depends on the system and the configuration file for re-compilation. Under the circumstances what is the best possible option? Should the relevant scripts read the system data base and then alter the name of the file and directories accordingly or is it a must to retain the 'i486' and one should go through the hard task of re-compiling the kernel. I am not getting any errors on Run_tests and 'mod4 model-default' but no file 1fdx.B9999001 is produced. Instead I get a core dump. Is this due to the low memory and swap space I have (32 MB each) or something else. Since I am going in single steps, I am receiving newer problems each time i go ahead with making the program run. Looking forward to hear from you (Andreji Sali) or any other linux user of MODELLER. Lutfullah

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Re: Modeller on linux
by Lutfullah Kakakhel 16 Oct '98

16 Oct '98

Hello again, Is it possible to increase the limit of 1000 on residues to about 1150 without switching to the larger moddler? I have the linux SMALL executable. Is the larger version available for LINUX? Lutfullah

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Re: Modeller on linux
by Lutfullah Kakakhel 15 Oct '98

15 Oct '98

>I am not sure what is going on without looking at your system ... > >Try this: > >cd /usr/local/bin/modeller4/bin >rm mod4 >mv mod4_linux-i486 mod4 ^ ^ 4? is this a typo? The one I found on the ftp site was mod_i486-linux-SMALL.Z >chmod a+x mod4 > >Also make sure /usr/local/bin/modeller4/bin is in your execution path >(echo $path). > Its now working. Strange as it may sound but my linux turns hosttype into i386-linux on its own no matter what you put in the .cshrc or even the system-wide /etc/profile. Each time I boot, the hosttype is turned into i386-linux. I used to force it into i486-linux in the step ./Install but then the script /bin/hosttype turns it back into i386-linux which gives an error on creation of the proper directory and "mod4" in its proper place thereby causing the subsequent errors i reported earlier. I changed your executable to mod_i386-linux (after all it is an executable) where it existed and apparently it has worked. Run_tests did not cause any error and has successfully gone through. I will try to find out where linux stores its machine type but may be there is no need. Thanks once again, Lutfullah >Best, Andrej > > >Lutfullah Kakakhel wrote: >> >> Thanks for your prompt reply. >> I am running csh and i have the suggested line in the .cshrc file. >> When I type: >> # hosttype i get the reply >> i486-linux >> when i type simply: >> #mod4 (with nothing else) i get >> /usr/local/bin/modeller4/bin/mod4: hosttype : command not found >> /usr/local/bin/modeller4/bin/mode: /usr/local/bin/modeller4/bin/mod_: no >> such file or directory. >> Have I installed the program in the right directories? >> >> I just copied the zipped archives to /usr/local and did whatever is written >> in the installation procedure. >> No error is generated till the end. But >> ./Run_tests >> produces the same errors: >> >> ./run_tops1:mod4: command not found >> >> Lutfullah >> >> -----Original Message----- >> From: Andrej Sali <sali(a)rockvax.rockefeller.edu> >> To: Lutfullah Kakakhel <seen(a)paknet2.ptc.pk> >> Cc: modeller_usage(a)salilab.org >> <modeller_usage(a)salilab.org> >> Date: Thursday, October 15, 1998 11:32 AM >> Subject: Re: Modeller on linux >> >> >Please define >> > >> >setenv HOSTTYPE i486-linux >> > >> >in your .cshrc file. >> > >> >Best, Andrej >> > >> > >> >> Lutfullah Kakakhel wrote: >> >> >> >> Hello, >> >> >> >> I just subscribed to the list and have the following to resolve: >> >> >> >> 1. I am trying to install MODELLER on a REDHAT 5.0 Linux system >> >> which is a Pentium 133MH, 32 MB RAM and 1.2 GB hard disk. Would it >> >> give me troubles >> >> later and if yes what kind? >> >> >> >> 2. The installation passes through all the stages successfully but >> >> i get a screenful of error messages: >> >> ./run_tops1: mod4: command not found >> >> when i try to test run as suggested in the documentation. >> >> >> >> 3. The system prompts a 'hosttype' i386-linux during the ./Install >> >> while the executable i have downloaded is mod_i486-linux. Which one >> >> would require change, if does? Does the above error has anything to >> >> do with this? >> >> >> >> Sorry if these sound dumb questions but i am totaly new in this field. >> >> >> >> >> >> Lutfullah >> >> >> >> >> > >> >-- >> >Andrej Sali, Assistant Professor >> >The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 >> >tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 >> >e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org >> > > >-- >Andrej Sali, Assistant Professor >The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 >tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 >e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org >

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Re: Modeller on linux
by Lutfullah Kakakhel 15 Oct '98

15 Oct '98

Thanks for your prompt reply. I am running csh and i have the suggested line in the .cshrc file. When I type: # hosttype i get the reply i486-linux when i type simply: #mod4 (with nothing else) i get /usr/local/bin/modeller4/bin/mod4: hosttype : command not found /usr/local/bin/modeller4/bin/mode: /usr/local/bin/modeller4/bin/mod_: no such file or directory. Have I installed the program in the right directories? I just copied the zipped archives to /usr/local and did whatever is written in the installation procedure. No error is generated till the end. But ./Run_tests produces the same errors: ./run_tops1:mod4: command not found Lutfullah -----Original Message----- From: Andrej Sali <sali(a)rockvax.rockefeller.edu> To: Lutfullah Kakakhel <seen(a)paknet2.ptc.pk> Cc: modeller_usage(a)salilab.org <modeller_usage(a)salilab.org> Date: Thursday, October 15, 1998 11:32 AM Subject: Re: Modeller on linux >Please define > >setenv HOSTTYPE i486-linux > >in your .cshrc file. > >Best, Andrej > > >> Lutfullah Kakakhel wrote: >> >> Hello, >> >> I just subscribed to the list and have the following to resolve: >> >> 1. I am trying to install MODELLER on a REDHAT 5.0 Linux system >> which is a Pentium 133MH, 32 MB RAM and 1.2 GB hard disk. Would it >> give me troubles >> later and if yes what kind? >> >> 2. The installation passes through all the stages successfully but >> i get a screenful of error messages: >> ./run_tops1: mod4: command not found >> when i try to test run as suggested in the documentation. >> >> 3. The system prompts a 'hosttype' i386-linux during the ./Install >> while the executable i have downloaded is mod_i486-linux. Which one >> would require change, if does? Does the above error has anything to >> do with this? >> >> Sorry if these sound dumb questions but i am totaly new in this field. >> >> >> Lutfullah >> >> > >-- >Andrej Sali, Assistant Professor >The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 >tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 >e-mail sali(a)rockvax.rockefeller.edu; http://salilab.org >

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Modeller on linux
by Lutfullah Kakakhel 14 Oct '98

14 Oct '98

Hello, I just subscribed to the list and have the following to resolve: 1. I am trying to install MODELLER on a REDHAT 5.0 Linux system which is a Pentium 133MH, 32 MB RAM and 1.2 GB hard disk. Would it give me troubles later and if yes what kind? 2. The installation passes through all the stages successfully but i get a screenful of error messages: ./run_tops1: mod4: command not found when i try to test run as suggested in the documentation. 3. The system prompts a 'hosttype' i386-linux during the ./Install while the executable i have downloaded is mod_i486-linux. Which one would require change, if does? Does the above error has anything to do with this? Sorry if these sound dumb questions but i am totaly new in this field. Lutfullah

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different structures
by Gulshat Ibragimova 13 Oct '98

13 Oct '98

Dear modellers: I had got some questions when I tried to build a model on a basis of 3 different structures. I used full_homol.top (or model.top) script of the Modeller4. The sequence identities were 59, 54, and 47%. The resolution of structures was 1.8 - 2 A. The alignment was perfect. Nevertheless, at the end of an optimization procedure, the objective function was ca.3000 - 4000. When I have used only one structure (with the sequence identity 59%), the same optimization procedure resulted in models with the objective function of 600 - 700. Probably, for this particular case only one structure was necessary. However, it is still unclear to me, why using different structures increased the objective function value by an order? Which role does the CLUSTER_CUT option play for the TRANSFER_XYZ command? Changing it to 1.0 (as recommended by Manual) didn't let the Modeller4 run. An error message was reported: trfxyz_E> structures not isomorphic: i,na,na",nr,nr" 2 1147 1129 150 144 What does it mean? Thanks in advance, Gulshat --------------------------------------------------------------------- Gulshat Ibragimova, Ph.D. EMBL, Postfach 102209 69012 Heidelberg, FRG Tel: +49 (0)6221 387466, Fax: +49 (0)6221 387517

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I need help
by A.Romani＠leonardo.biomed.unipr.it 10 Sep '98

10 Sep '98

-------- I'm able to perform the basics of building, but now I've few questions to improve my model. I'built the model with the top script below : _____________________________________________ INCLUDE # Include the predefined TOP routines SET ALNFILE = 'alignment.ali' # alignment filename SET SEQUENCE = 'my_sequence' SET LIBRARY_SCHEDULE = 1 SET MD_LEVEL = 'refine1' SET FINAL_MALIGN3D = 1 SET REPEAT_OPTIMIZATION = 5 SET RSTRS_REFINED = 5 SET MD_RETURN = 'MINIMAL' SET KNOWNS = 'knows1' 'knows2' 'knows3' # codes of the templates SET ATOM_FILES_DIRECTORY = '/disk2/modeller4/examples' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 20 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling _____________________________________________________________________________________ With this script am I sure to build an accurate model? Are there other stuff that I can do to improve my model? How can I transfer the heteroatoms from template to model? Thanking in advance Your faithfully Antonello Romani ________________________________ Antonello Romani Istituto di Patologia Generale Plesso Biotecnologico Integrato Universita' degli Studi di Parma via Volturno 39 43100 Parma Tel. +39 521 903 751 Fax. +39 521 903 742 E-mail : A.Romani(a)leonardo.biomed.unipr.it _______________________________

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Re: Modeling a loop
by Robert Jorissen 05 Aug '98

05 Aug '98

Dear fellow MODELLERs I have found that the problem mentioned by Tom Lee about modelling loops only occurs for the MSI version of MODELLER and not the academic version. I get around the problem by putting the following in the TOP file.: INCLUDE DEFINE_STRING VARIABLES = LOOP_CSRFILE LOOP_INI_MODEL SET SEQUENCE = 'aaa' SET MODEL = 'aaa.pdb' # initial model of the target : : The define_string... line is the only line to be added. I can't remember how I trouble-shot the problem as I fixed it a month ago. I believe this will fix Dr Lee's problem. Regards Rob -- ----------------------------------------------------- Robert Jorissen Ludwig Institute for Cancer Research P.O. BOX 2008, Royal Melbourne Hospital Parkville, Victoria 3050, Australia phone: ++61-3-9341-3155 fax: ++61-3-9341-1938 e-mail: Robert.Jorissen(a)ludwig.edu.au -----------------------------------------------------

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Modeling a loop
by Tom Lee 27 Jul '98

27 Jul '98

Hi, I have generated a model for my molecule. I'm trying to study a loop region in detail. I followed the instruction in FAQ of the manual and wrote the following Top file: ------------------------------------------------------------------------------- INCLUDE SET SEQUENCE = 'ASLA2' SET MODEL = 'ASLA2.B99990001.pdb' SET ATOM_FILES_DIRECTORY = './:../atom_files' SET OUTPUT_DIRECTORY = './' SET PDB_EXT = '.pdb' SET STARTING_MODEL = 20 SET ENDING_MODEL = 29 SET MD_LEVEL = 'refine1' SET RAND_SEED = -34871 CALL ROUTINE = 'loop' CALL ROUTINE = 'cluster', ID1 = 20, ID2 = 29 SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT = '49:' '76:', SELECTION_STATUS = 'initialize' RETURN END_SUBROUTINE ----------------------------------------------------------------------------- "ASLA2.B99990001.pdb" is the file generated by the previous Modeler run. "49" and "76" are the starting and ending residues of the loop region. I got an error message after running this job: ------------------------------------------------------------------------------- TOP______> 102 414 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP______> 103 415 SET ROOT_NAME = SEQUENCE TOP______> 104 416 RETURN TOP______> 105 591 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = '$(JOB).rsr', RESULT = LOOP_CSRFILE assgn___E> cannot assign a value to a value: ------------------------------------------------------------------------------- Do you know what went wrong? Thanks. Tom

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Modeller
by he＠msvax.mssm.edu 27 Jul '98

27 Jul '98

Dear Modellers: I got a problem when i'm modelling my protein. The situation is that: I found my protein (aam) has a partial similarity with 1nkl ('5:' ' 127:'), made a ali. file, and call routine ='model' or using "build_model" . I got a PDB format file or .ini file (for example aam.B999901 or aam.ini). Then, i try to transfer / or modify another segment of aam from a high similarity protein (1udg, '223:' '289:') without losing 1nkl ('5:' '127:') information in aam.ini file, but in vain. Could you tell me which commands fit this purpose? Thanks for help. Xingxuan He, MD. Associate Dept. of Human Genetics Mt. Sinai Medical Center

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