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 ? … [View More]

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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 … [View More]

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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 … [View More]

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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 … [View More]

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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 (… [View More]

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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 … [View More]

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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 … [View More]

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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!!!!!!!!!!!! ============================================… [View More]

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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 … [View More]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. [View Less]

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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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