April 2011 - modeller_usage

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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optimization script
by rjayashree13-science＠yahoo.co.in 22 Apr '11

22 Apr '11

The following script optimize.py is not working for me. It is giving an error in the line: is giving an error in this line: mdl.generate_topology<aln, sequence=code+'ini'> Please suggest. Script env = environ() env.edat.dynamic_sphere = True env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') code = 'unbound-scrwl' aln = alignment(env) mdl = model(env, file=code) aln.append_model(mdl, align_codes=code, atom_files=code) aln.append_model(mdl, align_codes=code+'-ini', atom_files=code+'.ini') mdl.generate_topology(aln, sequence=code+'-ini') mdl.transfer_xyz(aln) mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.write(file=code+'.ini') # Generate the restraints: mdl.restraints.make(aln, restraint_type='stereo', spline_on_site=False) mdl.restraints.write(file=code+'.rsr') mpdf = mdl.energy() mdl.switch_trace(file=code+'.trc') mdl.optimize(optimization_method=1, max_iterations=20, output='REPORT', trace_output=1) mdl.optimize(optimization_method=3, temperature=300, max_iterations=50, output='REPORT', trace_output=1) mdl.optimize(optimization_method=1, max_iterations=20, output='REPORT', trace_output=1) mpdf = mdl.energy() mdl.write(file=code+'.B') Dr. Jayashree RamanaLecturer, Department of Biotechnology and Bioinformatics Jaypee University of Information Technology Waknaghat, Solan Himachal Pradesh-173234 http://www.juit.ac.in/Department/bio/faculty_bio.php?faculty_id=118

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reading MRC origin coordinates in modeller and FLEX-EM
by dmitry lyumkis 21 Apr '11

21 Apr '11

Dear all, My question has to do with the way in which modeller / flex-em reads the coordinates of mrc maps and/or pdb files. I'm trying to use flex- em and have a PDB file fitted to a map with the following properties: boxsize = 144 pixelsize = 2.18 origin = -72, -72, -72 in pixels (or -156.96, -156.96, -156.96 in Angstroms) When I input either of the NEGATIVE values into the flex-em.py script, the program stalls while reading the model. When I input the coordinates in POSITIVE Angstroms, i.e. 156.96, 156.96, 156.96, (which is what is specified in flex-em.py), I receive an error: "Atom 1 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated", line 38 in conjugate gradients.py. When I input the coordinates in positive pixels, i.e. 72,72,72, the program seems to work fine, but translates the subsequent PDB files by a large amount that I cannot understand (i.e., NOT values of 72 or ~157). Finally, I tried changing the coordinate system of the map to 0,0,0, then saving the PDB file accordingly, and that seemed to work. Do I have to specify a 0,0,0 coordinate system every time, or is there an easier way around this issue? Best regards, Dmitry Lyumkis Automated Molecular Imaging Group, Department of Cell Biology The Scripps Research Institute 10550 North Torrey Pines Road c/o Dmitry Lyumkis, CB129 La Jolla, CA 92037 tel: (858) 784-9208; cell: (408) 772-1792; dlyumkis(a)scripps.edu; http://ami.scripps.edu

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Regarding alignment
by Ashish Runthala 21 Apr '11

21 Apr '11

Dear MODELLERS, MODELLER doesn't incorporate MSP based alignment consideration. I have two queries. 1. How to make MODELLER consider HSP to be extended on either side to generate. 2. How to generate a profile based best structural alignment of all considered templates against the target sequence. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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