September 2015 - modeller_usage

Conformational Modelling
by Parker de Waal 02 Oct '15

02 Oct '15

Hi Modeller users, I have an interesting case where I have two known structures of related proteins A and B. A is in the inactive conformation while B is in the active conformation. Is it possible to use modeller to predict the active conformation of A using structure B as the template? Further, despite being in different conformations, only a handful of residues are important for this conformational change (the rest remain stable and are distal from the active site). Is it possible to hold the correct parts of protein A in place and only perform modelling on residues within the active site (taken from protein B as template)? Best, Parker

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Model Building
by Wong Li Zhe 02 Oct '15

02 Oct '15

Dear all, I am trying to build a protein model. Is it possible to build the model with the generated PDB files (with lowest DOPE score). There are 2 regions I which to build, where the first region consist of 1 template & the second region consists of 7 templates. I have built 100 models each for the 2 regions using single template approach and multiple template approach for the latter. >From the 100 models, I pick the best model with lowest DOPE score. With that, I have 1 model for first region & 1 model for second region. I would like to use the generated 2 models, combine them to build a final model. To my understanding, I can't proceed straight to the 'model building' command as it doesn't append PDB file. And I was trying to generate the alignment file for the 2 models but it won't work either. Could any of you enlighten me on this? Thank you & have a nice day! Best regards, Li Zhe [http://imu.edu.my/e-banner/sew-2015.jpg] Explore the endless possibilities in the field of medicine & health sciences. Register today at http://info.imu.edu.my/sew

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Problem in oligomer modelling
by Soong Jiaxin 29 Sep '15

29 Sep '15

Hi all, I'm modelling a dodecamer. Somehow, there seems to be a problem for some of the monomers to connect to the other monomers. The oligomer template I used has interdimeric contacts. However, the way my model connects among the monomers is different from the template I used. The tail for the monomer in concern goes in and out of the beta strands of the neighbour monomer instead of connecting by touching the C-terminal region interface of the next monomer. Is there a way to fix this or is this normal for a protein model? I have attached a copy of my modelling script as well. Thank you for your help in advance. Regards, Vanessa

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using DSS/BS crosslink information as restrain
by thereal sisterdot 08 Sep '15

08 Sep '15

Dear modeller users and "caretakers", i was using modeller to model a heterohexameric complex from mouse where the yeast orthologous structure is known. to evaluate the models i used the DOPE score and visualized a dozen available intersubunit DSS/BS crosslinks using Xlink Analyzer in chimera. for 2 neighbouring subunit 3 crosslinks indicate that the published heterohexameric complex appears to have a different arrangement in that part than the published one (crosslinked residues between subunits are around 60A apart) in order to obtain a model satisfying those crosslink restrains would one add the 3 crosslinks as below, or can you recommend a better approach: class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Constrain the distance between alpha carbons in residues 611 chain D # and 224 chain B to be less than 30 angstroms: rsr.add(forms.upper_bound(group=physical.xy_distance, feature=features.distance(a['CA:611:D'], a['CA:224:B']), mean=30., stdev=0.1)) thanks a lot!!!! Maria

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Import error
by GaoKyle 08 Sep '15

08 Sep '15

Hi,I'm running win7 64bit, and have both 32bit python3.4 and modeller9.15 installed. I'm getting this error when I tried to run a simple script:-------------------------------------Traceback (most recent call last): File "D:\学习\论文\Methylation\modeller\fasta2pir.py", line 1, in <module> from modeller import * File "C:\Program Files (x86)\Modeller9.15\modlib\modeller\__init__.py", line 93, in <module> import _modellerImportError: DLL load failed: 操作系统无法运行 %1。-------------------------------------------Please ignore the Chinese. I really have no idea of how to fix this problem.Please advise me.Thank you !

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Sequence difference between alignment and PDB
by Wong Li Zhe 08 Sep '15

08 Sep '15

Dear all, I edited the alignment file (SF3B1-Mult.ali) and would like to generate a protein model. Edited the templates sequence accordingly to start from position 610-1198. It is however, I keep getting the error message 'sequence difference between alignment and PDB'. Being the first time Modeller user, would anyone be kind enough to guide me as to how I should rectify the problem. Hereby I attached the alignment file along with this email. Thank you. Best regards, Li Zhe [http://imu.edu.my/e-banner/od-aug.jpg] Come join our INFO DAYS. Your journey in healthcare starts here! Find out more at http://info.imu.edu.my/open-day#infodays

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回复： using DSS/BS crosslink information as restrain
by S～star 08 Sep '15

08 Sep '15

dts 发自我的iPhone ------------------ 原始邮件 ------------------ 发件人: thereal sisterdot <therealsisterdot(a)gmail.com> 发送时间: 2015年09月08日 14:27 收件人: modeller_usage <modeller_usage(a)salilab.org> 主题: Re: [modeller_usage] using DSS/BS crosslink information as restrain

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