- modeller_usage - salilab.org

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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RE : help with residues numbering
by BESSADOK Anis 27 Feb '09

27 Feb '09

Hi all, I'm a new user of modeller, I want to know how to conserve residue numbering between my target sequence and the MODEL? I will try to build a final Model using two parts of my protein sequence but I want to conserve the numbering. One of my alignment files looks like this: >P1;2hydA structureX:2hydA:1:A:578::::: ----------------------------------------------MIKRYLQFVKPYKY RIFATIIVGIIKFGIPMLIPLLIKYAIDGVINNHA----------------LTTDEKVHH LTIAIGIALFIFVIVRPPIEFIRQYLAQWTSNKILYDIRKKLYNHLQALSARFYA--NNQ VGQVISRVINDVEQTKDFILTGLMNIWLDCITIIIALSIMFFLDVKLTLAALFIFPFYIL TVYVFFGRLRKLTRERSQALAEVQGFLHERVQGISVVKSFAIEDNEAKNFDKKNTNFLTR ALKHTRWNAYSFAAINTVTDIGPIIVIGVGAYLAISGSITVGTLAAFVGYLELLFGPLRR LVASFTTLTQSFASMDRVFQLIDEDYDIKNG-VGAQPIEIKQGRIDIDHVSFQYNDN-EA PILKDINLSIEKGETVAFVGMSGGGKSTLINLIPRFYDVTSGQILIDGHNIKDFLTGSLR NQIGLVQQDNILFSDTVKENILLG-RPTATDEE-VVEAAKMANAHDFIMNLPQGYDTEVG ERGVKLSGGQKQRLSIARIFLNNPPILILDEATSALDLESESIIQEALDVLSKDRTTLIV AHRLSTITHADKIVVIENGHIVETGTHRELIAKQGAYEHLYSIQNL----* >P1;1pgp sequence:1pgp:43: :630::::: --------------------------------------------SNWLDKLYMVVGTLAA IIHGAGLPLMMLVFGEMTDIFANAGNLEDLMSNITNRSDINDT---GFFMNLEEDMTR-- ----YAYYYSGIGAGVLVAAYIQVSFWCLAAGRQIHKIRKQFFHAIMRQEIGWFD--VHD VGELNTRLTDDVSKINEGIGDKIGMFFQSMATFFTGFIVGFTRGWKLTLVILAISPVLGL SAAVWAKILSSFTDKELLAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNKNLEEAKRI GIKKAITANISIGAAFLLIYASYALAFWYGTTLVLSGEYSIGQVLTVFFSVLIGAFSVGQ ASPSIEAFANARGAAYEIFKIIDNKPSIDSYSKSGHKPDNIKGNLEFRNVHFSYPSRKEV KILKGLNLKVQSGQTVALVGNSGCGKSTTVQLMQRLYDPTEGMVSVDGQDIRTINVRFLR EIIGVVSQEPVLFATTIAENIRYGREN--VTMDEIEKAVKEANAYDFIMKLPHKFDTLVG ERGAQLSGGQKQRIAIARALVRNPKILLLDEATSALDTESEAVVQVALDKARKGRTTIVI AHRLSTVRNADVIAGFDDGVIVEKGNHDELMKEKGIYFKLVTMQT-----* Regards, A Anis PhD Student iBiTec-S/SB2SM Laboratoire Stress oxydant et Détoxication CEA-SACLAY, 91191 Gif-sur-Yvette cedex e-mail: anis.bessadok(a)cea.fr Tel (33)1-69084432, Fax (33)1-69088717

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Using modeller with a web form: how topass the provided key to modeller?
by Stéphane Téletchéa 20 Feb '09

20 Feb '09

Hello, I'm planning to provide models from carefully validated alignments and in order to provide this tool, i would like to allow users to access to the full model, and produce new ones using my methodology, from a web server. According to the policy, http://salilab.org/modeller/FAQ.html#18, i must use a form and use this key for launching modeller (i totally agree with this). However, how can i use this license? In fact, if i install modeller the standard way (on linux, using http://salilab.org/modeller/9v6/release.html#rpm) env KEY_MODELLER9v6=XXXX rpm -Uvh modeller-9v6-1.i386.rpm, then the key is incorporated in the installation. In this case, the "external" key is not used (mine is taken). On the other end, if i install modeller without the key (remove the env KEY_MODELLER9v6=XXXX to the above command), i receive: KEY_MODELLER9v5=<VALIDKEYHERE> /usr/bin/mod9v5 file.py Traceback (most recent call last): File "<string>", line 1, in ? File "/usr/lib/modeller9v5/modlib/modeller/__init__.py", line 65, in ? _modeller.mod_start() _modeller.ModellerError: check_lice_E> Invalid license key: xxx Go to http://salilab.org/modeller/ to get a license key, and then set the 'license' variable to it in the file /usr/lib/modeller9v5/modlib/modeller/config.py I have tried various combinations to set the KEY_MODELLER9v5 (env, export, in a sourced file, etc) but i'm always stucked. Any idea ? Thanks a lot in advance, Stéphane Téletchéa

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Academic and Commercial
by salam pradeep 18 Feb '09

18 Feb '09

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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Hydrogen name in modeller
by Xia,Wei 16 Feb '09

16 Feb '09

Dear all: I'm a new user to Modeller. It seems that the hydrogen names in Modeller results are HB1, HB2 However IUPAC and many other software would use 'HB2 HB3' names. Is there any options in Modeller that I can choose or any scripts to use to convert the format? Thanks! Xia Wei

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