January 2007 - modeller_usage

Cómo instalar MODELLER
by Carlos Lozano 11 Jan '07

11 Jan '07

Hola a todos de la comunidad, la primer pregunta que me surge, es que no tengo ni idea de cómo instalar MODELLER en mi ibook. Sí alguién puede recomendarme algún tip, se lo agradecería. Carlos

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origin of blosum62.sim.mat and as1.sim.mat
by Joshua A. Speidel 11 Jan '07

11 Jan '07

Hello, I am curious about the origin of the blosum62.sim.mat and as1.sim.mat. When I look at the blosum62.sim.mat, I can't figure out the relationship between the numbers there, and the original blosum62 matrix. Initially, I thought that the Henikoff & Henikoff values were just scaled to between 0 and 1000, but that didn't seem to work. I can't find a reference for ALBASE3 mentioned in as1.sim.mat. Finally, if I wanted to use my own matrix, is it necessary for me to scale it to between 0 and 1000? Your help in understanding this is greatly appreciated, Josh

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Re: [modeller_usage] Ligands
by Esben Jannik Bjerrum 09 Jan '07

09 Jan '07

Hi Joel Have you tried to include an @ in your alignment file?according to restyp.lib (in mollib directory) it should correspond to ATP. I dont know how about the quality of the parameters are, but its a starter. And theres a starter for tweaking in top_heav.lib. If theres no ATP (or similat molecule) in you template You'll need to add some constraints to some atoms between your protein and ATP to restrict it to a position near the binding site. Happy Modelling Esben Bjerrum __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Ligands
by Joel Tyndall 08 Jan '07

08 Jan '07

Hi all, I'm wanting to add in an ATP molecule based on my template to my modelled structure. I have looked at the FAQ and it does seem a laborious task to write the CHARM topology files etc. I was wondering if there was a database of ligands (wiki? type thing) or a web based converter ( i have already looked at Prodrg in dundee) or if someone wants to share their top files for ATP. ...Or any alternative methods out there? I'm currently using 8v2 but with old scripts and will upgrade soon. Cheers joel -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin 9054 New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034

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modeller model and modbase model
by hori koshii 07 Jan '07

07 Jan '07

Hi all, Has anyone come across with the models on MODBASE? How does that compare to our own models built by using "MODELLER"? (I know they are both using MODELLER, but the protein I am working on, have very different "insertion" loops from my results and modbase's) I have been trying to build a protein model using MODELLER8, but recently come across with one already available on the MODBASE. I think there is actually only one good template (over 30%) for my target. I used MODELLER 8 to build 1000 models and pick out the ones with lower DOPE scores. The loop conformations in my model and the one on MODBASE are quite different. I am curious espeically about the loop insertions. So, I am wondering how come they are very different? Could anyone from this forum give me any comment about this please? Thank you :) Sincerely yours, __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Problems about disulfide bonds
by 饶�� 03 Jan '07

03 Jan '07

Dear Mr.: I have some questions about two commonds model.patch_ss_templates() and model.patch_ss().First,I don't know what exactly does these two commonds want to do.In my opinion,the earler can indicate wether the disulfide bonds exist and where are they and the later has the same function of which the target is the protein which is modeled.But after I have run the commond and used the mdl.energy() commond,I don't how to understant the output file.I don't know what information I can get from the .log file. In fact,what I am doing now is to model a protein which has a hign homology with another protein of which the structure has been known.The template is thermophilic and has a disulfide bond.The target has two cys amino acids in the same places where the template form the disulfide bond.However,after the target model has been established,the Chimera software indicate that no disulfide bond exists.The target protein has no ability of thermostability.So I want to use the MODELLER software to explore the differences between them and find out what factors influence the target protein and make it can't be thermophilic.The disulfide bond is the first element I take into account. How do I solve the problems above? I am very appreciate your advises. Yours sincerely, Rao Ben __________________________________________________ 赶快注册雅虎超大容量免费邮箱? http://cn.mail.yahoo.com

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