May 2007 - modeller_usage

Re: [modeller_usage] Ubuntu installation issue
by Modeller Caretaker 15 May '07

15 May '07

carromeu(a)usp.br wrote: > Hi Modellers, > > I'm trying to install Modeller on Ubuntu 7.04. I follow the steps from the Ben's > answer, but I don't do the symlink. In true, I don't know how to do this. Any > help is welcome. Making the symlink is easy: assuming you already have the RPM installed, just do (as root, and all on one line) ln -sf /usr/lib/modeller9v1/modlib/modeller /usr/lib/python2.5/site-packages/ Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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problems modeling a multimer
by Douglas Kojetin 15 May '07

15 May '07

Hi All, I would like create a hexameric model using a target sequence and a hexameric PDB template. I am trying to create an alignment using input files that have the \ character to separate the chains. Example: >P1;target sequence:target:::::::0.00: 0.00 AAAAA\ BBBBB\ CCCCC\ DDDDD\ EEEEE\ FFFFF* I'm using the align2d.py example, as detailed in tutorial 2. My input PDB file has six chains (A-F). My align2d.py file is as follows: """ align2d.py START from modeller import * log.verbose() env = environ() aln = alignment(env) mdl = model(env, file='PDBfile_hexamer', model_segment= ('FIRST:A','LAST:F')) aln.append_model(mdl, align_codes='PDBfile_hexamer', atom_files='PDBfile_hexamer.pdb') aln.append(file='target_hexamer.ali', align_codes='target') aln.align2d() aln.write(file='target_hexamer-PDBfile_hexamer.ali', alignment_format='PIR') aln.write(file='target_hexamer-PDBfile_hexamer.pap', alignment_format='PAP') """align2d.py END Using modeller9v1 (linux RPM), I started the above calculation (python align2d.py), but it has not finished after 20 hours (and is still going; 100% CPU and 22.6% memory usage out of 3 GB total, according to 'top'). Although I used log.verbose(), there is very little output in the associated log (see below). Any ideas? Thanks, Doug """ LOG START MODELLER 9v1, 2007/01/19, r4822 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2007 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 carbo.msbb.uc.edu 2.6.18-1.2869.fc6 i686 Date and time of compilation : 2007/01/19 13:47:34 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2007/05/11 11:26:27 openf___224_> Open $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL9v1}/modlib/ resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL9v1}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3216122 3140.744 3.067 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3216650 3141.260 3.068 openf___224_> Open ${MODINSTALL9v1}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3265250 3188.721 3.114 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 ${MODINSTALL9v1}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3280562 3203.674 3.129 openf___224_> Open ${MODINSTALL9v1}/modlib/radii14.lib openf___224_> Open ${MODINSTALL9v1}/modlib/solv.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL9v1}/modlib/ af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL9v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL9v1}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL9v1}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL9v1}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL9v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> model.read(file='PDBfile_hexamer', (def) model_format='PDB', model_segment=('FIRST:A', 'LAST:F')) openf___224_> Open PDBfile_hexamer.pdb Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 7756771 7574.972 7.397 openf___224_> Open PDBfile_hexamer.pdb read_mo_297_> Segments, residues, atoms: 24 4818 38574 read_mo_298_> Segment: 1 4 A 234 A 1790 read_mo_298_> Segment: 2 246 A 271 A 214 read_mo_298_> Segment: 3 291 A 636 A 2799 read_mo_298_> Segment: 4 651 A 850 A 1626 read_mo_298_> Segment: 5 4 B 234 B 1790 read_mo_298_> Segment: 6 246 B 271 B 214 read_mo_298_> Segment: 7 291 B 636 B 2799 read_mo_298_> Segment: 8 651 B 850 B 1626 read_mo_298_> Segment: 9 4 C 234 C 1790 read_mo_298_> Segment: 10 246 C 271 C 214 read_mo_298_> Segment: 11 291 C 636 C 2799 read_mo_298_> Segment: 12 651 C 850 C 1626 read_mo_298_> Segment: 13 4 D 234 D 1790 read_mo_298_> Segment: 14 246 D 271 D 214 read_mo_298_> Segment: 15 291 D 636 D 2799 read_mo_298_> Segment: 16 651 D 850 D 1626 read_mo_298_> Segment: 17 4 E 234 E 1790 read_mo_298_> Segment: 18 246 E 271 E 214 read_mo_298_> Segment: 19 291 E 636 E 2799 read_mo_298_> Segment: 20 651 E 850 E 1626 read_mo_298_> Segment: 21 4 F 234 F 1790 read_mo_298_> Segment: 22 246 F 271 F 214 read_mo_298_> Segment: 23 291 F 636 F 2799 read_mo_298_> Segment: 24 651 F 850 F 1626 relabel_387W> Model has multiple chains, and they do not all have a unique chain ID. Suggest you relabel them as A, B, C, etc. runcmd______> alignment.append_model (atom_files='PDBfile_hexamer.pdb', align_codes='PDBfile_hexamer') Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 7896464 7711.391 7.531 Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 10639518 10390.154 10.147 runcmd______> alignment.append(align_codes=['PDBfile_hexamer', 'target'], atom_files=['PDBfile_hexamer.pdb'], file='target_hexamer.ali', (def)remove_gaps=True, (def) alignment_format='PIR', (def)rewind_file=False, (def)close_file=True) openf___224_> Open target_hexamer.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 12123550 11839.404 11.562 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 13607494 13288.568 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13607522 13288.596 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13607550 13288.623 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13607578 13288.650 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13607606 13288.678 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13607634 13288.705 12.977 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 13627070 13307.686 12.996 Read the alignment from file : target_hexamer.ali Total number of alignment positions: 4865 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------ ------- 1 PDBfile_hexa 4818 24 PDBfile_hexame undefined 2 target 4860 6 target runcmd______> alignment.align2d((def)overhang=0, (def)align_block=0, (def)rr_file='$(LIB)/as1.sim.mat', (def)align_what='BLOCK', (def) off_diagonal=100, (def)max_gap_length=999999, (def) local_alignment=False, (def)matrix_offset=0.0, (def)gap_penalties_1d= (-900.0, -50.0), (def)gap_penalties_2d=(3.5, 3.5, 3.5, 0.20000000000000001, 4.0, 6.5, 2.0, 0.0, 0.0), (def)surftyp=1, (def) fit=True, (def)fix_offsets=(0.0, -1.0, -2.0, -3.0, -4.0), (def) read_weights=False, (def)write_weights=False, (def) input_weights_file='', (def)output_weights_file='', (def)n_subopt=1, (def)subopt_offset=0.0, (def)read_profile=False, (def) input_profile_file='', (def)write_profile=False, (def) output_profile_file='', (def)weigh_sequences=False, (def) smooth_prof_weight=10, (def)weights_type='SIMILAR') align2d_276_> 'align_block' changed to 1. openf___224_> Open PDBfile_hexamer.pdb Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 13627550 13308.154 12.996 openf___224_> Open PDBfile_hexamer.pdb mkapsa__637W> No residue topology library is in memory. Better radii would be used if topology.read() is called first. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. openf___224_> Open $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 """ LOG END

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query about chimeric protein
by Sana Bilal 15 May '07

15 May '07

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query
by ajeeta kaushiki 15 May '07

15 May '07

Hi.. I am doing advance modelling with multiple template . I have to add ATP ang Mg in my structure . I am trying to add @ , $ for the purpose ,ATP hetero atom is present in the template even though its giving error . Can I add ATP in 1 of the template only . The error is - File "model_mult.py", line 9, in ? a.make() File "/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/automodel/automodel.py", line 108, in make self.homcsr(exit_stage) File "/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/automodel/automodel.py", line 416, in homcsr aln.check() File "/nfs/condor/home/ajeeta/bin/modeller9v1/modlib/modeller/alignment.py", line 154, in check libs=self.env.libs.modpt) _modeller.error: rdabrk__337E> Structure not read in... The log file is - runcmd______> alignment.append(align_codes=['2FFAA', '1XEFA', '2FFBA', 'CaNBD'], atom_files=[], file='CaNBD-mult.ali', (def)remove_gaps=True, (def)alignment_format='PIR', (def)rewind_file=False, (def)close_file=True) read_te_290E> Number of residues in the alignment and pdb files are different: 242 241 For alignment entry: 2 1XEFA x (mismatch at alignment position 242) Alignment KELLSEPESLYSYLYQLQSD@ PDB KELLSEPESLYSYLYQLQSD Match ******************** Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 2 1XEFA rdabrk__337E> Structure not read in (please consult the log file for more details): Please help. Thanks and Regards Ajeeta kaushiki JNU

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Optimizing the Helix strain in the model?
by Ngo Duc Tri 14 May '07

14 May '07

Dear Modeller users, I can learn from the Interative Example (Modeller Tutorial) that I can increase the accuracy of the helix strain by removing or transfering the gap to the begining or ending ot the helix. However If my alignment don't have the gap in the helix region and the alignment score seem maximum. I would like to know how I can do in this situation because optimizing the loop cannot be applied in this. This region is in the transmembrane of a membrane protein. Thank you very much for all of your advices, My best regards, TriNgo

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loop to connect two domain
by Jayapal, Prabha 14 May '07

14 May '07

Dear Modeller: I am new to protein modelling. I want to connect two domains by a loop containing 16 residues. I am having templates for both the domains and not for the loop. I have tried some of the loop modelling techniques but unsuccessful. Can anybody help me with this situation? Thanks in advance. Cheers J.Prabha

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getting pdb's but not fit.pdb's
by roac0030＠flinders.edu.au 09 May '07

09 May '07

hey, i'm new to modeller. I can use modeller and and get homology models of proteins but when it comes to writing the superposed pdb's (the x_fit.pdb's) it comes up with an error and doesn't... i've included the .top, .ali, and .pdb as well as a screenie of the error. any help would be greatly appreciated. thanks heaps -mike

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Modeller as webservice (WSDL)
by Francoijs, Kees-Jan 09 May '07

09 May '07

L.S, I'm currently using modeller as standalone application but 'm planning to set up a more automated setup. To do this i wanted to use modeller as a webservice (WSDL) in Taverna. Has any body ever created a wrapper for this? In the archives no reference to wsdl found :-( Thanx in advance Kees-Jan

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[Fwd: Cannot generate the plot of DOPE?]
by Modeller Caretaker 08 May '07

08 May '07

-------- Original Message -------- Subject: Cannot generate the plot of DOPE? Date: Wed, 9 May 2007 02:03:18 +0900 From: Ngo Duc Tri <ngoductri(a)gmail.com> To: modeller-care(a)salilab.org Dear Modeller users, I finished modelling my protein and doing the evaluation step. I run the file evaluate_model.py to calculate the DOPE score of my model. I got DOPE score : -39521.605469 and there was no error in the log file. I use this profile file to generate the DOPE plot using GNUPLOT but this program show a strange line. Actually It just show the position of my aminoacid but no DOPE score for each. I run the GNUPLOT and used the command: plot ' myprotein.profile' I want to ask you If it's the error of GNUPLOT or my profile file? And how can i fix it to show the actual DOPE score for each residues. Thank you very much for your comments, Best regards, TriNgo Sungkyunkwan University

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Ubuntu installation issue
by Christian Meesters 07 May '07

07 May '07

Hi, I just installed Ubuntu 7.04 on one machine and tried to get modeller running. I tried an installation from source as well as using the rpm. Actually modeller itself is installed, but the python module is not available. The only python-installation I have is 2.5 and I would rather not work with 2.3. Last time I installed modeller I had the module running with python 2.4, so I guess running with 2.5 should be possible, too. (There are no .so-files I could get into the python path manually.) Did anyone try to install modeller on Ubuntu/Debian or alike and has a hint for me? TIA Christian

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