May 2011 - modeller_usage

Need help regarding alteration of align2d.py parameters
by Ashish Runthala 02 May '11

02 May '11

Dear Modellers, Align2d.py the pairwise alignment is not working i want it to. Will somebody please tell me where are the options to change the considered score matrix and other gap based parameters. Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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High energy in template-based parts of the model
by Lilit Nersisyan 02 May '11

02 May '11

Hi, I am building a protein model based on templates and secondary structure restraints. My protein is 781 amino acids long, and it has two homology derived templates in the 1-92 and 394-412 segments. The 590-781 segment has a solved crystallographic structure. I have given the corresponding templates to these three segments. I have also added secondary structure restraints to the remaining parts of the protein based on secondary structure predictions. The problem is that when I plot the DOPE profiles of the generated models, I see that the template-based segments (especially the 590-781 segment) have the highest energy. This makes it impossible to refine only the parts of the model with high energy, since the refinement will destroy the structures that must be present in the protein. I have used the standard scripts for model making and restraint-adding incorporated in Modeller examples. I would like to know the reasons for getting high energy in the part of the protein, which has a solved crystallographic structure. I will appreciate any advice. Thank you. -- Lilit Nersisyan Institute of Molecular Biology NAS RA E-mail: txgt.lilit.nersisyan(a)gmail.com Tel.: +37494 601703

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batch model building
by Vagmita Pabuwal 02 May '11

02 May '11

Hi, I was wondering if we can build models in batch if we are using same template, but different alignment, so for each alignment we have new model. And this could be automated.I have to build around 300 models with same template but different alignment for each model i generate. I would really appreciate if anybody could help me on this. Otherwise it takes a long time if I build them using automodel, as each time i have to change the .ali filename and also the sequence name in there. ThanksVagmita

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