- modeller_usage - salilab.org

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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one question about merging two proteins into one
by zhangliqun 26 Apr '11

26 Apr '11

Dear modeller administrator: I tried to merge two protein dimers into one dimer, with only 7 residues overlapped in each monomer. The aligned.ali file is like following: >P1;pl5t structureX:pl5t: 1 : :+78 : :::-1.00:-1.00 GESPGAFPVAAQVGLGVGTSLLALGVIIIVLMYRRKSKQ---------------------------GESPGAFPVAAQVGLGVGTSLLALGVIIIVLMYRRKSKQ---------------------------* >P1;pbjm structureX:pbjm: 1 : :+68 : :::-1.00:-1.00 --------------------------------YRRKSKQALRDYKKVQIQLENLESSVRDRCKKEF--------------------------------YRRKSKQALRDYKKVQIQLENLESSVRDRCKKEF* >P1;plxd sequence:plxd GESPGAFPVAAQVGLGVGTSLLALGVIIIVLMYRRKSKQALRDYKKVQIQLENLESSVRDRCKKEFGESPGAFPVAAQVGLGVGTSLLALGVIIIVLMYRRKSKQALRDYKKVQIQLENLESSVRDRCKKEF* I also have the obtain_structure.py file like following: from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../../atom_files'] a = automodel(env, alnfile = 'alignment.ali', knowns = 'pl5t', sequence = 'plxd') a.starting_model= 1 a.ending_model = 1 #a.loop.starting_model = 1 #a.loop.ending_model = 2 #a.loop.md_level = refine.fast a.make() Above files are built based on instructions online. But when I used mod9v8 obtain_structure.py command, I got following error message: MODELLER 9v8, 2010/04/21, r7145 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2010 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA 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 karplus3 2.6.35.12-88.fc14.x86_64 x86_64 Date and time of compilation : 2010/04/21 09:44:36 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2011/04/26 17:37:48 openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234076 3158.277 3.084 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234604 3158.793 3.085 openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283204 3206.254 3.131 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL9v8}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292444 3215.277 3.140 openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v8}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3303901 3226.466 3.151 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3305351 3227.882 3.152 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3308251 3230.714 3.155 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3369383 3290.413 3.213 parse_pir__E> Invalid PIR file header line: sequence:plxd There should be 10 fields separated by colons, : This line actually contains 2 fields. I really do not know how to solve the problem. Could you give me some help on that? Thank you very much. Best, lqz

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modelling coordinate of missing residues
by Sangita Kachhap 26 Apr '11

26 Apr '11

Hello all I have a pdb file and coordinate of 13 amino acid (N-terminal arm)are missing in this pdb file. Is it possible to generate coordinte of these missing residue? I have a pdb file of other protein of same family in this pdb file N-terminus is random coil and turn and in my query pdb N-terminus is random coil and 3-10 helix. I have predicted the secondary structure for missing residues they are random coil and sequence identity is of query with template except N-terminal is 68%. So is it possible to model a protein of query sequence using above mension known pdb file? Sangita Kachhap JRF BIC,IMTECH CHANDIGARH

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Regarding Salign Alignment
by Ashish Runthala 25 Apr '11

25 Apr '11

Dear Modellers, I am facing a small problem. Alignments are not coming the way i expect. Is there any way that when i change the alignments to be glocal based on BLOSUM80 scores. It first do local and then proceed for optimum global alignments. I AM MESSED UP WITH SHIFTED ALIGNMENT PROBLEMS. Thanks, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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