- modeller_usage - salilab.org

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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How to run flexEM package parallel
by ruiz＠berkeley.edu 20 Apr '11

20 Apr '11

Hi, Ben, I am using the flexEM package in modeller to refine a large complex. However, it took a long time for one CG/MD cycle. I wonder can I run the job in parallel ? Maybe you can directly edit the script below. Thanks! Rui # ============================================================================ # # a. Define the type of oprimization: conjugate gradients minimization (CG) # or molecular dynamics (MD) # b. Edit input parameters: density map parameters and probe structure # # ======================= Maya Topf, 4 Dec 2007 ============================= from modeller import * import shutil import sys, os, os.path import string import math from CG import opt_cg from MD import opt_md env = environ() ############### INPUT PARAMETERS ################## optimization = 'MD' # type of optimization: CG / MD rigid_filename = 'rigid.txt' # rigid bodies file name path = './' # directory path code = '1ake' # 4 letter code of the structure input_pdb_file = '1ake_init.pdb' # input model for optimization em_map_file = '1ake_10A.mrc' # name of EM density map (mrc) format='MRC' # map format: MRC or XPLOR apix=1.0 # voxel size: A/pixel box_size=69 # size of the density map (cubic) resolution=10.0 # resolution x=-9.0; y=14.0; z=-8.0 # origin of the map num_of_runs = 1 # number of runs initial_dir = 1 ############### RUN OPTIMIZATION ################## # CG # ---- if optimization == 'CG': for i in range(initial_dir,initial_dir+num_of_runs): scratch = path + '/' + str(i) + '/' os.system("mkdir -p " + scratch) os.system("cp " + path + '/'+ input_pdb_file + " " + scratch) os.chdir(scratch) opt_cg(path, code, str(i), 55*i, em_map_file, input_pdb_file, format, apix, box_size, resolution, x, y, z, rigid_filename) # MD # ---- elif optimization == 'MD': for i in range(initial_dir,initial_dir+num_of_runs): scratch = path + '/' + str(i) + '/' # input_pdb_file = 'final' + str(i) + '_cg.pdb' # os.chdir(scratch) opt_md(path, code, str(i), 10*i, em_map_file, input_pdb_file, format, apix, box_size, resolution, x, y, z, rigid_filename)

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restrict salign to subparts of some structures sequences
by Benjamin SCHWARZ 20 Apr '11

20 Apr '11

Hello modellers, I have a very large dataset of (beta propeller domain) structures, which I inspected visually to assess parts that sounded obviously not relevant for a structural alignment. For some structures I spotted long loops or several small helices insertions which I would like salign not to consider during the structural alignment. Is there a way to do so ? thanks --Ben.S

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Re: [modeller_usage] Long loop modeling
by bharat lal 20 Apr '11

20 Apr '11

Hi, I want to know whether long loop modeling of 30 or 40 residue length is possible through modeller or not ??.. ---------- Bharat

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 73
by Ashish Runthala 20 Apr '11

20 Apr '11

Dear Ramana, There is a script optimize.py. But MD+SA is already working. You won't get contrasting significant better model decoy. Run MODELLER for longer run to select decoy as per 3D-Jury or any other clustering method. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Wednesday, April 20, 2011 2:50:13 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 73 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: Long loop modeling (bharat lal) 2. restrict salign to subparts of some structures sequences (Benjamin SCHWARZ) 3. How to run flexEM package parallel (ruiz(a)berkeley.edu) 4. (no subject) (rjayashree13-science(a)yahoo.co.in) ---------------------------------------------------------------------- Message: 1 Date: Fri, 15 Apr 2011 19:06:26 +0530 (IST) From: bharat lal <monu46010(a)yahoo.com> Subject: Re: [modeller_usage] Long loop modeling To: modeller <modeller_usage(a)salilab.org> Message-ID: <650005.60727.qm(a)web94712.mail.in2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I want ?to know whether long loop modeling of 30 or 40 residue length is possible through modeller or not ??.. ----------? Bharat

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