October 2009 - modeller_usage

ERROR ALIGN_CODES
by Leonardo Herrera 22 Oct '09

22 Oct '09

Hi modeller user's I have a problem when I am realising my model with multiple templates, in the step to align the alignment of pdb's versus my sequence I obtain the following problem… Traceback (most recent call last): File "align2d_mult.py", line 14, in <module> aln.append(file='Tc30.ali', align_codes='giAAR00925') File "/usr/lib/python2.6/site-packages/modeller/alignment.py", line 79, in append allow_alternates) _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 13) = giAAR00925 I could'nt find an answer to this problem, it already changes the format (fasta to pir ...), and code several times (giAAR00925 to 13... to c30 ...), so please can somebody help with this error message? thanks in advance My script is from modeller import * log.verbose() env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') # Read aligned structure(s): aln = alignment(env) aln.append(file='alineamiento.ali', align_codes='all') aln_block = len(aln) # Read aligned sequence(s): aln.append(file='Tc30.ali', align_codes='giAAR00925') # Structure sensitive variable gap penalty sequence-sequence alignment: aln.salign(output='', max_gap_length=20, gap_function=True, # to use structure-dependent gap penalty alignment_type='PAIRWISE', align_block=aln_block, feature_weights=(1., 0., 0., 0., 0., 0.), overhang=0, gap_penalties_1d=(-450, 0), gap_penalties_2d=(0.35, 1.2, 0.9, 1.2, 0.6, 8.6, 1.2, 0., 0.), similarity_flag=True) aln.write(file='Tc30-mult.ali', alignment_format='PIR') aln.write(file='Tc30-mult.pap', alignment_format='PAP') my Tc30.ali is giAAR00925 524 residues MGRLQRFSAFVPLTLSFISQASAAIGPVTDLTISDADISPDGFTRAAVVMNDQFPGPLIAGNKGDNFQINVI DNLSNSTMLTSTTIHWHGFFQKGTNWADGAAFVNQCPISAGNSFLYDFTATDQAGTFWYHSHLSTQYCDGLR GPMVVYDPDDPHASLYDVDDDSTVITLSDWYHTAARLGARFPAGADSTLINGLGRAAGGDADAALAVFNVTQ GSRYRFRLVSLSCDPNFNFTIQDHNMTIIEVDGVNVEPVTVDSIQIFAGQRYSFVLTADQDIGNYWIQAVPN TGTVTTDGGVNSAILRYDTADPIEPDAADPTSSIPLVETDLVPLENLAAPGDPTVGGVDLAMNLEFDFNGTW FFINGEPFVPPSVPVLLQIMSGAQSAADLLPSGSVYTLPANSTIEISFPMNTTAAPGAPHPFHLHGHTFYVV RSAGSTEYNYVNPPQRDTVSTGTDGDNVTIRFTTNNPGPWFLHCHIDFHLDAGFAIVLSEDTPDAASANTPS SAWDDLCPTYNTDYPDGLGR* and my alineamiento.ali is >P1;1gw0.10wA structureX:1gw0.10w_fit.pdb: 1 :A:+573 :A:::-1.00:-1.00 --EPTCNTPSNRACWSDGFDINTDYEVSTPDTGVTQSYVFNLTEVDNWMGPDGVVKEKVMLINGNIMGPNIVANW GDTVEVTVINNLV----TNGTSIHWHGIHQKDTNLHDGANGVTECPIPPKGGQRTYRWRAR-QYGTSWYHSHFSA QYGNGVVGTIQING---PASLPYDID--LGVFPITDYYYRAADDLVHFTQN-----NAPPFSDNVLINGTAVNPN TGEGQYANVTLTPGKRHRLRILNTSTENHFQVSLVNHTMTVIAADMVPVNAMTVDSLFLAVGQRYDVVIDASRAP -DNYWFNVTFGGQAACGG-----SLNPH----PAAIFHYAGAPGGLPTDEGTPPVDHQCLDTLDVRPVVPRSV-- PVNSFVKRPDNTLPVALDLTGTPLFVWKVNGSDINVDWGKPIIDYILTGN------TSYPVSDNIVQVDAVDQWT YWLIENDPEGPFSLPHPMHLHGHDFLVLGRSPDVPAASQQ-RFVFDPAVDLARLNGDNPPRRDTTMLPAG---GW LLLAFRTDNPGAWLFHCHIAWHVSGGLSVDFLERPADLRQRISQEDEDDFNRVCDEWRAYWPTNPYPKIDSGL-- ----------------------....wwwwwwwwww* >P1;1gyc.10wA structureX:1gyc.10w_fit.pdb: 1 :A:+513 :A:::-1.00:-1.00 AI--------------------------------GPAASLVVANA--PVSPDG-FLRDAIVVNGVFPSPLITGKK GDRFQLNVVDTLTNHTMLKSTSIHWHGFFQAGTNWADGPAFVNQCPIAS-GHSFLYDFHVPDQAGTFWYHSHLST QYCDGLRGPFVVYDPKDPHASRYDVDNESTVITLTDWYHTAARLGPR----------FPLGADATLINGLGRSAS TPTAALAVINVQHGKRYRFRLVSISCDPNYTFSIDGHNLTVIEVDGINSQPLLVDSIQIFAAQRYSFVLNANQTV -GNYWIRANPN--F---------GTVGFAGGINSAILRYQGAPVAEPTTTQTTS-VIP-LIETNLHPLARMPVPG SPTPGGVDKALNLAFNFNG-----TNFFINNASFTPP-TVPVLLQILSG---AQTAQDLLPAGSVYPLP-AHSTI EITLPATA-LAPGAPHPFHLHGHAFAVVRSAGS----------------T--TYNYNDPIFRDVVSTGTPAAGDN VTIRFQTDNPGPWFLHCHIDFHLEAGFAIVFAEDVADVKAA--NPVPKAWSDLCPIYDGLSEANQ---------- ----------------------....wwwwwwwwww* >P1;1kya.10wA structureX:1kya.10w_fit.pdb: 1 :A:+513 :A:::-1.00:-1.00 GI--------------------------------GPVADLTITNA--AVSPDG-FSRQAVVVNGGTPGPLITGNM GDRFQLNVIDNLTNHTMLKSTSIHWHGFFQKGTNWADGPAFINQCPISS-GHSFLYDFQVPDQAGTFWYHSHLST QYCDGLRGPFVVYDPNDPAADLYDVDNDDTVITLVDWYHVAAKLGPA----------FPLGADATLINGKGRSPS TTTADLSVISVTPGKRYRFRLVSLSCDPNYTFSIDGHNMTIIETDSINTAPLVVDSIQIFAAQRYSFVLEANQAV -DNYWIRANPN--F---------GNVGFTGGINSAILRYDGAAAVEPTTTQTTS-TAP-LNEVNLHPLVATAVPG SPVAGGVDLAINMAFNFNG-----TNFFINGASFTPP-TVPVLLQIISG---AQNAQDLLPSGSVYSLP-SNADI EISFPATA-AAPGAPHPFHLHGHAFAVVRSAGS----------------T--VYNYDNPIFRDVVSTGTPAAGDN VTIRFRTDNPGPWFLHCHIDFHLEAGFAVVFAEDIPDVASA--NPVPQAWSDLCPTYDARDPSDQ---------- ----------------------....wwwwwwwwww* -- MenB Leonardo David Herrera Zúñiga POSGRADO EN QUÍMICA UAMI Biofisicoquímica Universidad Autonoma Metropolitana Iztapalapa Tel. +52 (55) 5804 4674

1 0

Rebuilding pdball.pir file for mod9v1
by Praveen Raj 22 Oct '09

22 Oct '09

Hi, I would like to know how can we rebuild a new pdball.pir file (for Modeller9v1) from a local copy of PDB files. Please suggest a feasible method to rebuild pdball.pir with the same syntax supported by mod9v1. Thanks in advance for any help Praveen.

2 1

building a model with zn ions
by anu priya 21 Oct '09

21 Oct '09

Hi all, My target protein has two zinc atoms. I aslo obtain the binding sites of these metals in my target sequence. how do i incorporate these zn ions in to my modelled structure? Is it appropriate to include zn ions after modelling or is it neccessary to include it before modelling? Also please give me a procedure to do this like example script files or alignment files or any alternative methods. Thank you. -- G.Anupriya, Research student, National university of singapore.

2 1

ubuntu installation with python 2.6
by Knut J Bjuland 20 Oct '09

20 Oct '09

I have install modeller by following the instruction. An I symlink to /usr/lib/python2.6/site-package. Is there any thing else I might have forgotten to symlink knutb@phenylalanine:~/modeller/basic-example$ python build_profile.py Traceback (most recent call last): File "build_profile.py", line 1, in <module> from modeller import * ImportError: No module named modeller _________________________________________________________________ Windows Live: Make it easier for your friends to see what you’re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

2 1

Parallel modeller
by Hugo Gutiérrez de Teran 13 Oct '09

13 Oct '09

Hi, I want to run parallel job on my Quadcore. I used as a template the script provided in the examples/automodel/model-parallel.py But I get the following error: File "loopmodel.py", line 3, in ? from modeller.parallel import * File "/usr/lib/modeller9v5/modlib/modeller/parallel/__init__.py", line 1, in ? from job import job File "/usr/lib/modeller9v5/modlib/modeller/parallel/job.py", line 1, in ? import socket, random, os, select ImportError: No module named socket Thanks for help, Hugo -- Hugo G. de Teran, PhD. "Parga Pondal" Research fellow Fundación Pública Galega de Medicina Xenómica - SERGAS Santiago de Compostela (SPAIN) Phone +34 981563100 ext 13873 e-mail:hugo.teran@usc.es http://web.usc.es/~hugogdt

2 5

Modeling ligands in the binding site
by Qinghua Liao 12 Oct '09

12 Oct '09

Hi modeller users, I want to build a model with a ligand in the binding sites, but I have problems. I read the manual on-line, but I don't find any python script for aligning the sequence to the structure with ligand. I don't know the differences when compared to structure without ligand. Could somebody give me some example of these python script, or give me some suggestion on how to edit the python script which is used to align to structure without ligand? Thanks very much! ALl the best, qinghua

2 1

Help with iterative modelling tutorial
by Jonathan Harris 09 Oct '09

09 Oct '09

2 1

request a clear method for modelling a dimeric protein
by Othman Houcemeddine 09 Oct '09

09 Oct '09

Dear sir; I am trying to use modeller to predict the structure of a dimeric protein with no obvious symmetry between each of its subunits. My BLAST search shows that the first subunit alpha is homologous to a monomeric protein "C", while the other subunit beta is homologous to another different monomeric protein "D". Basically, I tried to align alpha with "C" and beta with "D" and I decided that the best strategy is to use a typical script from the tutorial"Building a model from multiple templates". I am not quite sure that this procedure is the best way to build my model. Also, I found a problem in writing my alignment file especially the header section and the assignment of each of the subunits to each of the templates. Could any body verify my alignment file and give me a clear method to deal with this situation? Thanks Alignment file.ali: >P1;alpha&beta sequence:alpha&beta:1:A:142:B:::: --xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx/ ------xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx* >P1;C; structureX:C: 1:A:58: : : : : xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-------------/ -------------------------------------------------------------------------------* >P1;D structureX: D:1:A:78::::: -----------------------------------------------------------------------------/ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx* script file: # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './' a = automodel(env, alnfile = 'Alignment file.ali', # alignment filename knowns = ('C', 'D'), # codes of the templates sequence = 'proteinX') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling OTHMAN Houcemeddine Pasteur Institute of Tunis - Tunisia othmanhoucemeddine(a)yahoo.fr

2 1

Helix rotation
by Liam Browne 05 Oct '09

05 Oct '09

I have a question about the most effective way of modelling a protein that is in a different conformation to the structure? I am hoping to make a homology model, then rotate a helix about its center and allow modeller to remake the model (allow energy minimisation etc) to determine the effects on the whole protein. Is there a way to do this? _________________________________________________________________ View your other email accounts from your Hotmail inbox. Add them now. http://clk.atdmt.com/UKM/go/167688463/direct/01/

2 1