March 2009 - modeller_usage

Combining steps in Basic and Advanced Tutorial ?
by Ashika Umanga Umagiliya 04 Mar '09

04 Mar '09

Dear Modeller caretaker, I follow the steps 1 and 2 in the 'Basic tutorial'. Then using the generated 'build_profile.prf' during step 2; I select upto maximum 5 templates with lowest e-value. Then I proceed with steps on 'Advanced tutorial'.ie in 'salign.py', I use above selected templates for modelling.. How accurate is my procedure? Best Regards, Umanga -- アシカウマンガウマギリヤ㈱国際バイオインフォマティクス研究所（BiGG) 〒140-0001 東京都品川区北品川3-6-9 アンドウビル8F TEL:03-6679-8763 FAX:03-6679-8764

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Completing missing residues
by Lee Soin 04 Mar '09

04 Mar '09

Hello, all! I have a PDB file that has several consecutive residues missing. Can MODELLER help to complete them? And how? Thanks! -- SUN Li Department of Physics Nanjing University, China

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Modeller and DNA-protein complexes.
by Chaix Denis 03 Mar '09

03 Mar '09

Dear ALL I want to use have Modeller, DNA-protein complexes. I have a structure of a protein:DNA as a template and the sequence of an unknown dna binding protein structure I have already made the alignement Could modeller model the unknown protein and the unknown DNA structure? What is the good protocol to obtain a good model Best, Denis -- CHAIX Denis Centre de Biochimie Structurale INSERM U554/CNRS 5048 29 rue de Navacelles F-34090 Montpellier, France Tel: 33 4 67 41 77 21 Fax: 33 4 67 41 79 13 e-mail:Denis.chaix@cbs.cnrs.fr http://www.cbs.cnrs.fr

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Histidine protonation state with allhmodel
by Jean Didier Pie Marechal 03 Mar '09

03 Mar '09

Dear All, I am building a model with a specific zinc coordination sphere. I decided to use a full atom run and this actually improved the overall quality of the models. I have a problem though. In the structure, the zinc is chelated by several histidines some by delta others by epsilon chelating modes. However, the resulting models are always with the same protonation state (epsilon). This leads to undesired clashes. How can I stipulate modeller to use a given protonation state with the charmm force field. Should I use the charmm residue code in the initial pdb? Or should I define this in the python script. Thanks for any help Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: modeller_usage-request(a)salilab.org Data: Divendres, Febrer 20, 2009 4:02 pm Assumpte: modeller_usage Digest, Vol 8, Issue 12 > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. Academic and Commercial (salam pradeep) > 2. Re: Academic and Commercial (Modeller Caretaker) > 3. Using modeller with a web form: how topass the provided key > to modeller? (St?phane T?letch?a) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 18 Feb 2009 15:12:48 +0530 > From: salam pradeep <salampradeep(a)gmail.com> > Subject: [modeller_usage] Academic and Commercial > To: modeller_usage(a)salilab.org > Message-ID: > <901340f20902180142w8dd888nc1b6e9a2be8ce262(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Is there any variation in the models generated by the Academic > version and > the Commercial version of Modeller. > Some people say that the Modeller Academic version is not so > accurate in > generating the 3D models. > How far is it true. >

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loop modeling based on a template
by Marco Neves 03 Mar '09

03 Mar '09

Hi, I have two pdb files of the same protein in complex with different ligands. PDB1 has all residues. PDB2 misses a small loop. Is it possible to model the missing loop of PDB2 based on the corresponding residues of PDB1 while keeping all other residues in the exact same positions? Which functions should be used? Thank you very much! marco neves

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modeling question
by Jean-Paul Armache 03 Mar '09

03 Mar '09

Hello, I would like to pose a question. I am doing homology modeling of various proteins, some of which are really straightforward to model, others, due to some issues, not. I have a problem in this case: a protein has one or several folded domains and long, unstructured parts that are connecting them. Sometimes on those unstructured parts are very small folded parts, sometimes not. What is critical for me is to model these unstructured parts as close to the original template as possible. Instead, I land up with models with these loops that are going all ways but the way it was in the template. This happens also in the situation when two sequences have really high identities and similar lengths. Is there a way to tell Modeller to model these parts as close to the model as possible? Best regards, Jean-Paul Armache

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