- modeller_usage - salilab.org

align-template.py command erorr
by Sajad Ahrari 18 May '11

18 May '11

hello dears I am trying to build a model of protein1 with MG-ATP(naturally 1 holds ADP instead of MG-ATP in it's structure) , based on protein2 structure witch holds MG-ATP in it's structure(2 is considered as template). in fact I want only hetero-atoms of protein2 be considered and finally be added to the structure of 1, by modeller. i have prepared the PDB file of both 1and2 .but after running the command"mod9v8 align-templates" , I am faced with this erorr " import site' failed; use -v for traceback". could you please let me know what is wrong?( I have attached the "align-templates.py" file, to be considered for any possible mistakes in it) thanks in advance! sajad

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Re: [modeller_usage] Problem in mGeneThreader link
by Bishwajit Das 16 May '11

16 May '11

On Mon, May 16, 2011 at 11:06 PM, Bishwajit Das <das.bishwajit(a)gmail.com>wrote: > Dear modeller > i want to submit my sequence into mGeneThreader,but i doin't > get the link.please send me the mGeneThreader server link where i submit my > query to finding fold assignment. > > Thanking You. > > -- > * > > > BISHWAJIT DAS*** > KOLKATA > > -- * BISHWAJIT DAS* *+91-9433237920* KOLKATA

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FATAL ERROR: MODINSTALL9v9 environment variable not set: incomplete MODELLER installation on Ubuntu 10.4
by crina ionescu 10 May '11

10 May '11

Hi. I am trying to run Modeller under Ubuntu and I am getting the following output: ----------- Running calculation: /usr/lib/modeller9.9/bin/mod9.9_i386-intel8 model.py MODELLER outputs: FATAL ERROR: MODINSTALL9v9 environment variable not set: incomplete MODELLER installation ---------- I had a look through the archives for similar issues, but the solution was posted only for Windows. Either I'm the only one who managed to mess it up under Linux, or I'm the only one who isn't able to fix it. In any case, I'd love some help. I installed Modeller in the following way. I downloaded the corresponding package (modeller_9.9-1_i386.deb) and just opened it. The package manager ran the installation itself (I did not do it in the terminal). ------ Selecting previously deselected package modeller. (Reading database ... 307463 files and directories currently installed.) Unpacking modeller (from .../modeller_9.9-1_i386.deb) ... Setting up modeller (9.9-1) ... Modeller installed, but not licensed. Please visit the Modeller web site at http://salilab.org/modeller/ to get a license key, and then edit the file /usr/lib/modeller9.9/modlib/modeller/config.py to set the key, i.e. the line license = 'xxx' should be changed to read license = 'MYKEY' where MYKEY is the key you obtained. ------- I then got a key and edited the respective file accordingly. Was I supposed to run anything else after this? All the best. Crina

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Need help regarding alteration of align2d.py parameters
by Ashish Runthala 02 May '11

02 May '11

Dear Modellers, Align2d.py the pairwise alignment is not working i want it to. Will somebody please tell me where are the options to change the considered score matrix and other gap based parameters. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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High energy in template-based parts of the model
by Lilit Nersisyan 02 May '11

02 May '11

Hi, I am building a protein model based on templates and secondary structure restraints. My protein is 781 amino acids long, and it has two homology derived templates in the 1-92 and 394-412 segments. The 590-781 segment has a solved crystallographic structure. I have given the corresponding templates to these three segments. I have also added secondary structure restraints to the remaining parts of the protein based on secondary structure predictions. The problem is that when I plot the DOPE profiles of the generated models, I see that the template-based segments (especially the 590-781 segment) have the highest energy. This makes it impossible to refine only the parts of the model with high energy, since the refinement will destroy the structures that must be present in the protein. I have used the standard scripts for model making and restraint-adding incorporated in Modeller examples. I would like to know the reasons for getting high energy in the part of the protein, which has a solved crystallographic structure. I will appreciate any advice. Thank you. -- Lilit Nersisyan Institute of Molecular Biology NAS RA E-mail: txgt.lilit.nersisyan(a)gmail.com Tel.: +37494 601703

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batch model building
by Vagmita Pabuwal 02 May '11

02 May '11

Hi, I was wondering if we can build models in batch if we are using same template, but different alignment, so for each alignment we have new model. And this could be automated.I have to build around 300 models with same template but different alignment for each model i generate. I would really appreciate if anybody could help me on this. Otherwise it takes a long time if I build them using automodel, as each time i have to change the .ali filename and also the sequence name in there. ThanksVagmita

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B value
by Sanger 28 Apr '11

28 Apr '11

Dear friends, I have some questions about the B value, generated from the Modeller along with the homology model. I am not sure how the temperature factor (Beta) is calculated (by MD simulation?). Since many homology modeling program didn't supply the information of B value, or just used it as a temporary space to fill up data, I am curious how serious the Modeller deals with it? Is it a proper data to estimate the flexibility of residues? Any suggestions or comments are greatly appreicated. Your sincerely, Xinhao Ye ---------- PhD candidate Department of Biological Systems Engineering, Virginia Tech Blacksburg, VA 24061 USA

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error in using a simulated structure as template.
by Bala subramanian 28 Apr '11

28 Apr '11

Friends, I am a newbie to modeller. I have the structure of a protein obtained from MD simulation (total 339 residues). I have another sequences of unknown structure ( total 345 residues). I want to model the structure of the later by using the simulated structure as template. I first aligned the two sequences with clustwal and made the .ali file (pasted below) . The modeller script i used is attached. Kindly write me what is going wrong ? *The following is the ali file.* >P1; temp structureM:temp:1 :A:339 :A :::: VVLENVTEHFNMWKNDMVEQMQEDIISLWDQSLKPCVKLTPLCVGAGSCDTSVITQACPK ISFEPIPIHYCAPAGFAILKCNDKTFNGKGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAE EEVVIRSDNFTNNAKTIIVQLKESVEINCTRPNQNTRKSIHI--GPGRAFYTTGEIIGDI RQAHCNISRAKWNDTLKQIVIKLREQF-ENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCN SAQLFNSTWNN---NTEGSNNTEG-NTITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCS SNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIE* >P1; targ sequence:targ:::::::: VVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVITQACPK VSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAE EEVVIRSANFTDNAKTIIVQLNQSVEINCTRPNNNTRKSIRIQRGPGRAFVTIGK-IGNM RQAHCNISRAKWNATLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCN STQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQFINMWQEVGKAMYAPPISGQIRCS SNITGLLLTRDGGNNNNGSEIFRPGGGDMRDNWRSELYKYKVVKIE* *I get the following error when i run the command mod9v8 model.py* 'import site' failed; use -v for traceback Traceback (most recent call last): File "model.py", line 11, in ? a.make() File "/apps/modeller/9v8//modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/apps/modeller/9v8//modlib/modeller/automodel/automodel.py", line 424, in homcsr self.check_alignment(aln) File "/apps/modeller/9v8//modlib/modeller/automodel/automodel.py", line 406, in check_alignment aln.check() File "/apps/modeller/9v8//modlib/modeller/alignment.py", line 200, in check self.check_structure_structure(io=io) File "/apps/modeller/9v8//modlib/modeller/alignment.py", line 209, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : Thanks, Bala

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Re: [modeller_usage] Downloads in an Intel core i7 system
by Esben Jannik Bjerrum 27 Apr '11

27 Apr '11

Hi David What Linux system are you using? Ubuntu or other debian based? The hint about using alien suggests so. alien is a tool that tries to convert rpm packages to deb packages before installation on debian based systems. Success is however not guaranteed. If its correct that you are using e.g. ubuntu try to use alien first, then install the generated .deb package. Best Regards Esben

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Downloads in an Intel core i7 system
by davidmanas 27 Apr '11

27 Apr '11

Dear Modeller Enthusiasts, I am trying to download Modeller to an Intel core i7 system for use with multiple CPUs. I am using the command suggested at the installation website: "rpm -Uvh modeller-9.9-1.x86_64.rpm". Then I get the following: =========================== rpm: RPM should not be used directly install RPM packages, use Alien instead! rpm: However assuming you know what you are doing... error: Failed dependencies: /bin/sed is needed by modeller-9.9-1.ia64 glib2 >= 2.2.0 is needed by modeller-9.9-1.ia64 /bin/sh is needed by modeller-9.9-1.ia64 /usr/bin/python is needed by modeller-9.9-1.ia64 libc.so.6.1()(64bit) is needed by modeller-9.9-1.ia64 libc.so.6.1(GLIBC_2.2)(64bit) is needed by modeller-9.9-1.ia64 libc.so.6.1(GLIBC_2.3)(64bit) is needed by modeller-9.9-1.ia64 libdl.so.2()(64bit) is needed by modeller-9.9-1.ia64 libdl.so.2(GLIBC_2.0)(64bit) is needed by modeller-9.9-1.ia64 libdl.so.2(GLIBC_2.1)(64bit) is needed by modeller-9.9-1.ia64 libglib-2.0.so.0()(64bit) is needed by modeller-9.9-1.ia64 libm.so.6.1()(64bit) is needed by modeller-9.9-1.ia64 libm.so.6.1(GLIBC_2.2)(64bit) is needed by modeller-9.9-1.ia64 libpthread.so.0()(64bit) is needed by modeller-9.9-1.ia64 libpthread.so.0(GLIBC_2.2)(64bit) is needed by modeller-9.9-1.ia64 libutil.so.1()(64bit) is needed by modeller-9.9-1.ia64 libutil.so.1(GLIBC_2.0)(64bit) is needed by modeller-9.9-1.ia64 =============================== I do know that /bin/sed, /bin/sh and /usr/bin/python are all downloaded in my system. I cannot understand why I am getting these errors. For the 64 bit libraries, I would like to know how to acquire them correctly. Thanks.

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