October 1998 - modeller_usage

problem!
by Paola D'Alessio 15 Jun '01

15 Jun '01

Dear users, I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have. When I tell Modeller to execute the "check_alignment" command, I get the following message: rdpir___E> alignment sequence not found in PDB file: 1 ./pXXXX.pdb ####################################################################################################################################### The alignment I have is: >P1;pXXXX structureX:pXXXX:.::.::::: CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM* >P1;pAveM structure:pAveM:2::211::::: -----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV* >P1;Ali2 sequence:Ali2:::::::: VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV* ####################################################################################################################################### Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb) Can somebody help me? Thank you very much, Paola -- dott. Paola D'Alessio (PhD student) Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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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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