April 2006 - modeller_usage

PDB id's found in buildtarget.py is missing in sequence database??
by Robert Selwyne 30 Apr '06

30 Apr '06

Good Day!!!!!!!!! I have a doubt, that modeller searches the best templates with respect to our target sequence in the sequence database using the command $mod8v2 buildtarget.py Now i make my comparetarget.py by adding the best five template's PDB i.d's as i got from buildtarget.log $mod8v2 comparetarget.py i get these errors!!!!!!!!!!!! ============================================================================= Traceback (most recent call last): File "compare target.py", line 7, in ? aln.malign3d() File "/usr/lib/modeller8v2/modlib/modeller/alignment.py", line 210, in malign3d io=io.modpt, libs=libs.modpt, **vars) File "/usr/lib/modeller8v2/modlib/modeller/util/top.py", line 93, in malign3d return _modeller.malign3d(aln, io, libs, *args) _modeller.error: malign3_682E> Structural information is not available for all sequences in the alignment. Aborting. ============================================================================ I am surprised to see the error -structural information is not available. It means the PDB i'ds are missing in the sequence database?. But those PDB id.s are taken from my buildtarget.log. How can i execute compare target.log? Now I have downloaded the necessary PDB files manually, Could you tell which/where directory to paste these files with a detailed command list since i am beginner to modeller. With Regards Robert Selwyne.

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The First African Structural Biology Conference
by skwofie＠mail.biotech.uwc.ac.za 30 Apr '06

30 Apr '06

The First African Structural Biology Conference Macromolecular Structure, Health and Biotechnology in Developing Countries The Wilderness, South Africa 24-27 October 2006 The First African Structural Biology (FASB) conference will be held in The Wilderness, South Africa. The conference will focus on the contributions and potential contributions of Structural Biology to the development of science and the creation of wealth in Africa with some emphasis on biotechnology and the alleviation of the disease burden of Africa. In particular, the conference has the following aims: 1. To promote structural biology in Africa, particularly in South Africa 2. To discuss contributions to the relief of disease, especially, TB, AIDS and malaria that have been made through an understanding of macromolecular structure 3. To provide the opportunity for South African students and scientists to meet and interact with some of the leading Structural Biologists in several fields that are relevant to our continent 4. To explore the merit and practicality of studying macromolecular structure in Africa 5. To discuss strategic and funding policies for structural biology and benchmark South Africa against other developing countries, notably Brazil and India 6. To identify projects of interest to the South African community in which structural analysis could play a role. The early registration deadline is 1 May 2006. Abstracts are due on 31 August 2006 Expression of interest and registration forms can be submitted online by visiting our website: http://sbio.uct.ac.za/conference Plenary lecturers: Tom Blundell (http://www-cryst.bioc.cam.ac.uk/~tom/) M. Vijayan (http://mbu.iisc.ernet.in/~mv/ ) Ed Egelman (http://www.people.virginia.edu/~ehe2n/) Peter Kwong (http://www.niaid.nih.gov/vrc/labs_kwong.htm) Joachim Frank (http://www.wadsworth.org/resnres/bios/frank.htm) Helen Saibil (http://people.cryst.bbk.ac.uk/~ubcg16z/) Igor Polikarpovhttp://www.if.sc.usp.br/pessoal/Gera_PadraoProf.msql?cod_obj=1178) Iain Campbell (http://www.ocms.ox.ac.uk/idc/) Gert Vriend (http://swift.cmbi.ru.nl/gv/) David Rice (http://www.shef.ac.uk/mbb/academic/staff/rice.html) James A. Sacchettini (http://puffer.tamu.edu/) Andreas Hoenger http://www.embl-heidelberg.de/ExternalInfo/hoenger/Hoenger_index.html) Krishna Murthy (http://main.uab.edu/show.asp?durki=34977) Ravi Acharya (http://www.bath.ac.uk/~bsssi/cgi/ravi_main.pl) Karolin Luger http://www.bmb.colostate.edu/faculty_detailed.cfm?lastname=Luger&firstname=K) Steve Bryant http://www.ncbi.nlm.nih.gov/Structure/RESEARCH/res.shtml) Christian Sommerhoff (http://webinfo.campus.lmu.de/view_person.cfm?ps=27095&cl=12) Conference Organizer: Trevor Sewell Institute of Infectious Disease and Molecular Medicine Wolfson Pavilion, Level 3 Faculty of Health Sciences University of Cape Town Anzio Road Observatory, 7925 South Africa Tel.: +27-21-6502817 Fax: +27-21-6891528 E-mail: sewell(a)uctvms.uct.ac.za Conference Organizing Committee: Dr Arvind Varsani (arwind(a)science.uct.ac.za) Professor Girish Kotwal (gkotwal(a)curie.uct.ac.za) Professor Ed Sturrock (sturrock(a)curie.uct.ac.za) Dr Muhammed Sayed (msayed(a)uwc.ac.za) Dr David Pugh (dpugh(a)uwc.ac.za) Miss Eulashini Chuntharpursat (eulashini(a)uctbc1.uct.ac.za) Mrs Miranda Waldron (mwaldron(a)uctvms.uct.ac.za) Miranda Waldron, Electron Microscope Unit, University of Cape Town, South Africa Tel +944 (0)21 650 2818 Fax +944 (0)21 689 1528

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FThe First African Structural Biology Conference
by skwofie＠mail.biotech.uwc.ac.za 30 Apr '06

30 Apr '06

The First African Structural Biology Conference Macromolecular Structure, Health and Biotechnology in Developing Countries The Wilderness, South Africa 24-27 October 2006 The First African Structural Biology (FASB) conference will be held in The Wilderness, South Africa. The conference will focus on the contributions and potential contributions of Structural Biology to the development of science and the creation of wealth in Africa with some emphasis on biotechnology and the alleviation of the disease burden of Africa. In particular, the conference has the following aims: 1. To promote structural biology in Africa, particularly in South Africa 2. To discuss contributions to the relief of disease, especially, TB, AIDS and malaria that have been made through an understanding of macromolecular structure 3. To provide the opportunity for South African students and scientists to meet and interact with some of the leading Structural Biologists in several fields that are relevant to our continent 4. To explore the merit and practicality of studying macromolecular structure in Africa 5. To discuss strategic and funding policies for structural biology and benchmark South Africa against other developing countries, notably Brazil and India 6. To identify projects of interest to the South African community in which structural analysis could play a role. The early registration deadline is 1 May 2006. Abstracts are due on 31 August 2006 Expression of interest and registration forms can be submitted online by visiting our website: http://sbio.uct.ac.za/conference Plenary lecturers: Tom Blundell (http://www-cryst.bioc.cam.ac.uk/~tom/) M. Vijayan (http://mbu.iisc.ernet.in/~mv/ ) Ed Egelman (http://www.people.virginia.edu/~ehe2n/) Peter Kwong (http://www.niaid.nih.gov/vrc/labs_kwong.htm) Joachim Frank (http://www.wadsworth.org/resnres/bios/frank.htm) Helen Saibil (http://people.cryst.bbk.ac.uk/~ubcg16z/) Igor Polikarpovhttp://www.if.sc.usp.br/pessoal/Gera_PadraoProf.msql?cod_obj=1178) Iain Campbell (http://www.ocms.ox.ac.uk/idc/) Gert Vriend (http://swift.cmbi.ru.nl/gv/) David Rice (http://www.shef.ac.uk/mbb/academic/staff/rice.html) James A. Sacchettini (http://puffer.tamu.edu/) Andreas Hoenger http://www.embl-heidelberg.de/ExternalInfo/hoenger/Hoenger_index.html) Krishna Murthy (http://main.uab.edu/show.asp?durki=34977) Ravi Acharya (http://www.bath.ac.uk/~bsssi/cgi/ravi_main.pl) Karolin Luger http://www.bmb.colostate.edu/faculty_detailed.cfm?lastname=Luger&firstname=K) Steve Bryant http://www.ncbi.nlm.nih.gov/Structure/RESEARCH/res.shtml) Christian Sommerhoff (http://webinfo.campus.lmu.de/view_person.cfm?ps=27095&cl=12) Conference Organizer: Trevor Sewell Institute of Infectious Disease and Molecular Medicine Wolfson Pavilion, Level 3 Faculty of Health Sciences University of Cape Town Anzio Road Observatory, 7925 South Africa Tel.: +27-21-6502817 Fax: +27-21-6891528 E-mail: sewell(a)uctvms.uct.ac.za Conference Organizing Committee: Dr Arvind Varsani (arwind(a)science.uct.ac.za) Professor Girish Kotwal (gkotwal(a)curie.uct.ac.za) Professor Ed Sturrock (sturrock(a)curie.uct.ac.za) Dr Muhammed Sayed (msayed(a)uwc.ac.za) Dr David Pugh (dpugh(a)uwc.ac.za) Miss Eulashini Chuntharpursat (eulashini(a)uctbc1.uct.ac.za) Mrs Miranda Waldron (mwaldron(a)uctvms.uct.ac.za) Miranda Waldron, Electron Microscope Unit, University of Cape Town, South Africa Tel +944 (0)21 650 2818 Fax +944 (0)21 689 1528

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The First African Structural Biology Conference]]
by skwofie＠mail.biotech.uwc.ac.za 30 Apr '06

30 Apr '06

The First African Structural Biology Conference Macromolecular Structure, Health and Biotechnology in Developing Countries The Wilderness, South Africa 24-27 October 2006 The First African Structural Biology (FASB) conference will be held in The Wilderness, South Africa. The conference will focus on the contributions and potential contributions of Structural Biology to the development of science and the creation of wealth in Africa with some emphasis on biotechnology and the alleviation of the disease burden of Africa. In particular, the conference has the following aims: 1. To promote structural biology in Africa, particularly in South Africa 2. To discuss contributions to the relief of disease, especially, TB, AIDS and malaria that have been made through an understanding of macromolecular structure 3. To provide the opportunity for South African students and scientists to meet and interact with some of the leading Structural Biologists in several fields that are relevant to our continent 4. To explore the merit and practicality of studying macromolecular structure in Africa 5. To discuss strategic and funding policies for structural biology and benchmark South Africa against other developing countries, notably Brazil and India 6. To identify projects of interest to the South African community in which structural analysis could play a role. The early registration deadline is 1 May 2006. Abstracts are due on 31 August 2006 Expression of interest and registration forms can be submitted online by visiting our website: http://sbio.uct.ac.za/conference Plenary lecturers: Tom Blundell (http://www-cryst.bioc.cam.ac.uk/~tom/) M. Vijayan (http://mbu.iisc.ernet.in/~mv/ ) Ed Egelman (http://www.people.virginia.edu/~ehe2n/) Peter Kwong (http://www.niaid.nih.gov/vrc/labs_kwong.htm) Joachim Frank (http://www.wadsworth.org/resnres/bios/frank.htm) Helen Saibil (http://people.cryst.bbk.ac.uk/~ubcg16z/) Igor Polikarpovhttp://www.if.sc.usp.br/pessoal/Gera_PadraoProf.msql?cod_obj=1178) Iain Campbell (http://www.ocms.ox.ac.uk/idc/) Gert Vriend (http://swift.cmbi.ru.nl/gv/) David Rice (http://www.shef.ac.uk/mbb/academic/staff/rice.html) James A. Sacchettini (http://puffer.tamu.edu/) Andreas Hoenger http://www.embl-heidelberg.de/ExternalInfo/hoenger/Hoenger_index.html) Krishna Murthy (http://main.uab.edu/show.asp?durki=34977) Ravi Acharya (http://www.bath.ac.uk/~bsssi/cgi/ravi_main.pl) Karolin Luger http://www.bmb.colostate.edu/faculty_detailed.cfm?lastname=Luger&firstname=K) Steve Bryant http://www.ncbi.nlm.nih.gov/Structure/RESEARCH/res.shtml) Christian Sommerhoff (http://webinfo.campus.lmu.de/view_person.cfm?ps=27095&cl=12) Conference Organizer: Trevor Sewell Institute of Infectious Disease and Molecular Medicine Wolfson Pavilion, Level 3 Faculty of Health Sciences University of Cape Town Anzio Road Observatory, 7925 South Africa Tel.: +27-21-6502817 Fax: +27-21-6891528 E-mail: sewell(a)uctvms.uct.ac.za Conference Organizing Committee: Dr Arvind Varsani (arwind(a)science.uct.ac.za) Professor Girish Kotwal (gkotwal(a)curie.uct.ac.za) Professor Ed Sturrock (sturrock(a)curie.uct.ac.za) Dr Muhammed Sayed (msayed(a)uwc.ac.za) Dr David Pugh (dpugh(a)uwc.ac.za) Miss Eulashini Chuntharpursat (eulashini(a)uctbc1.uct.ac.za) Mrs Miranda Waldron (mwaldron(a)uctvms.uct.ac.za) Miranda Waldron, Electron Microscope Unit, University of Cape Town, South Africa Tel +944 (0)21 650 2818 Fax +944 (0)21 689 1528

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(no subject)
by Robert Selwyne 27 Apr '06

27 Apr '06

Good Day!!!!!!!!! I had installed modeller software in my computer. I was practising the basic commands. I am comfortable till executing the command. $mod8v2 Target_profile.py Execution was successful and I got the information for Target_profile.log and Target_profile.prf as described in the tutorial. But to the next step when i run the command $mod8v2 Target_compare.py i get these errors!!!!!!!!!!!! ============================================================================= Traceback (most recent call last): File "Target_compare.py", line 7, in ? aln.malign3d() File "/usr/lib/modeller8v2/modlib/modeller/alignment.py", line 210, in malign3d io=io.modpt, libs=libs.modpt, **vars) File "/usr/lib/modeller8v2/modlib/modeller/util/top.py", line 93, in malign3d return _modeller.malign3d(aln, io, libs, *args) _modeller.error: malign3_682E> Structural information is not available for all sequences in the alignment. Aborting. ============================================================================ I have downloaded the necessary PDB files manually, Could you tell which/where directory to paste these files with a detailed command list since i am beginner to modeller. With Regards Robert Selwyne.

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Modelling of the interface of a protein complex
by Karsten SUHRE 27 Apr '06

27 Apr '06

Dear Modeller users, To study the interface between two proteins in complex (A+B), i.e. to decide whether these proteins may form a complex, I wish to compute a homology model on the basis of an existing, but only remotely homologous, complex (A'+B'), i.e. there are difference in some indels close to the interface. Each of the target proteins has also a closely homologous template, (A" and B"), which I would like to use to model the indels. However, as I am particularly interested in the interface, it is crucial to model the sidechains at the interface correctly, that is to account for the presence of the binding partner. Thus, the remote homologue (A+B) bears some important information as what concerns the complex. The most direct approach would be to use all templates and let MODELLER decide what to do. But is this really the optimal approach? Thank you very much in advance for any suggestion, or reference to similar problems. Kind regards, Karsten.

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Problem with evaluate_model.py
by Eva María Priego 26 Apr '06

26 Apr '06

Dear users, I am trying to obtain the DOPE potential and the corresponding plot for my best model. I am using the evalute_model.py script from the web tutorial, but when I run it I get this error: Traceback (most recent call last): File "evaluate_model.py", line 24, in ? normalize_profile=True, smoothing_window=15) TypeError: assess_dope() got an unexpected keyword argument 'output' Can somebody help me?. Thanks a lot in advance. I am using Modeller 8v0 and here is my scritp (my alignment file is called Ara.ali and the templates structures are located in ../templates/) from modeller import * 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 env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters # directories for input atom files env.io.atom_files_directory = '../templates/' # read model file mdl = model(env) mdl.read(file='Ara.B99990012.pdb') aln = alignment(env) code = "Ara" # generate topology aln.append_model(mdl, atom_files='Ara.B99990012.pdb', align_codes=code) aln.append_model(mdl, atom_files='Ara.B99990012.pdb', align_codes=code+'-ini') mdl.generate_topology(aln, sequence=code+'-ini') mdl.transfer_xyz(aln) mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='Ara.profile', normalize_profile=True, smoothing_window=15)

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Regarding > Compare.py < execution
by Robert Selwyne 26 Apr '06

26 Apr '06

ello Modeller Good Day!!!!!!!!! I had installed modeller software in my computer. I was practising the examples on basic modeling with my file name Target.ali, I am comfortable till executing the command. $mod8v2 Target.py Execution was success and I got the information for Target.log and Target.prf as described in the tutorial. But to the next step when i ran the command for comparision $mod8v2 Targetcompare.py i got these errors!!!!!!!!!!!! ============================================================================= [robert@cmm0 basic-example]$ mod8v2 Targetcompare.py Traceback (most recent call last): File "Targetcompare.py", line 6, in ? aln.malign3d() File "/usr/lib/modeller8v2/modlib/modeller/alignment.py", line 210, in malign3d io=io.modpt, libs=libs.modpt, **vars) File "/usr/lib/modeller8v2/modlib/modeller/util/top.py", line 93, in malign3d return _modeller.malign3d(aln, io, libs, *args) _modeller.error: malign3_682E> Structural information is not available for all sequences in the alignment. Aborting.[robert@cmm0 basic-example]$ ============================================================================ Could you please help me in getting rid of this error. I once again thank you for your kind service. With Regards Robert Selwyne.

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Problem with modeller8v2
by Ludovic Pétain 26 Apr '06

26 Apr '06

Hello, I have a problem with MODELLER8v2. Traceback (most recent call last): File "TASSERvsGPR43.py", line 15, in ? a.make() File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\loopmodel.py", l ine 28, in make automodel.make(self, exit_stage) File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\automodel.py", l ine 100, in make self.homcsr(exit_stage) File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\automodel.py", l ine 318, in homcsr aln = self.read_alignment() File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\automodel.py", l ine 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "M:\People\LPetain\Modeller8v2\modlib\modeller\alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "M:\People\LPetain\Modeller8v2\modlib\modeller\alignment.py", line 68, in __int_append libs=libs.modpt, **vars) File "M:\People\LPetain\Modeller8v2\modlib\modeller\util\top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = tasser I have seen in the same problem in the problem list (http://salilab.org/archives/modeller_usage/2006/msg00162.html) But I don't understand this problem since my script is: from modeller.automodel import * log.verbose() env=environ() class myloop(loopmodel): def select_loop_atoms(self): self.pick_atoms(selection_segment=('145:','173:'),selection_status='INITIALIZE') a=myloop(env,alnfile='TASSER_GPR43.ali',knowns='tasser', sequence='GPR43') a.starting_model=1 a.ending_model=1 a.md_level=None a.loop.strating_model=1 a.loop.ending_model=5 a.loop.md_level=refine.fast a.make() and it must be correct. Coulp you please help me? Thanks by advance. Ludovic PETAIN Trainee in Chemoinformatics EUROSCREEN SA Tel +32 71 348 500 Fax +32 71 348 519 Direct +32 71 348 509 http://www.euroscreen.com <http://www.euroscreen.com> This message contains information that may be confidential and privileged and is intended solely for the use of the intended recipient. Unless you are the intended recipient (or authorized to receive for the intended recipient), you may not use, copy or disclose to anyone the message and any attachments or any information contained in the message. If you have received this message in error, please notify Euroscreen at +32 71 348 500 or by reply e-mail and destroy all copies of this message and any attachments.

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Mutiple protein templates
by Sivaram I 25 Apr '06

25 Apr '06

Hi All I have a sequence.Its has about 300 aminoacids.The first 200 aa share sequence homology with one protein and the rest 100 share with other protein .Is there a way to build Homology model using the two protein structures .If yes how do I do it? Thanks in advance Sivaram

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