February 2009 - modeller_usage

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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Same alignment + different arch = different structure?
by Christopher Kauffman 10 Feb '09

10 Feb '09

I have been running a bunch of experiments with modeller 9v2 and noticed a strange behavior. For the same target-template alignment but a different computer, the structure that is produced by modeller varies. This probably has something to do with the random starting point being affected by the random number generation, maybe modeller links to slightly different libraries on different platforms. Has anyone else noticed this type of behavior and if so have they found a way to circumvent it? I have tried this on a couple flavors of 64-bit linux and a 32-bit linux as well, all 3 having slightly different results. Cheers, Chris

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Modeller 9v6 release
by Modeller Caretaker 09 Feb '09

09 Feb '09

The new version of Modeller, 9v6, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9v6 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v6 is primarily a bugfix release relative to the last public release (9v5). Major user-visible changes include: # Support for Python 2.6. # Support for sequence databases containing more than 2 billion residues. # Bugfixes to support compressed files on Windows systems, and fixes for density.grid_search(). See the Modeller manual for a full change log: http://salilab.org/modeller/9v6/manual/node38.html If you encounter bugs in Modeller 9v6, please see http://salilab.org/modeller/9v6/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Building a model from multiple templates ?
by Ashika Umanga Umagiliya 05 Feb '09

05 Feb '09

Greetings , After went through the Basic tutorial , I wanted to build a model from multiple templates (as shown at http://www.salilab.org/modeller/manual/node21.html) For that it says "-- simply provide an alignment between all of the templates and..." So to create the alignment between all of the templates,I modified the script "align2d.py" of step 3 (Aligning TvLDF with the template) in Basic tutorial , as follows: ------------------------------------------------------------- from modeller import * env = environ() aln = alignment(env) #modified from here to add several templates #template 1 mdl = model(env, file='1bdm', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='1bdmA', atom_files='1bdm.pdb') #template 2 mdl = model(env, file='1b8p', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='1b8pA', atom_files='1b8p.pdb') #template 3... #template 4... aln.append(file='TvLDH.ali', align_codes='TvLDH') aln.align2d() aln.write(file='TvLDH-mult.ali', alignment_format='PIR') aln.write(file='TvLDH-mult.pap', alignment_format='PAP') ------------------------------------------------------------- Then using the generated "TvLDH-mult.ali" file I am going to do the automdelling with multiple templates. Is this process correct? Thanks in advance. Umanga

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Fully automate the modelling process?
by Ashika Umanga Umagiliya 04 Feb '09

04 Feb '09

Greetings all, I am new to Modeller and in the application I am developing , I have to fully automate the modelling process.That mean,use only provide the Sequence (in simple FASTA) format and I want Modeller to generate structures for the sequence. I saw that I can use 'automodel' class ,but I dont know the procedure before using that class. thanks in advance, PS : Sorry for the newbie question , I come from Computer science background.

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No log file output
by Haslina Hashim 04 Feb '09

04 Feb '09

Hi, I'm using Modeller 9v5 on a linux machine and have run the model-single.py program. It ran successfully and the output was on the screen and when it finished running there is no model-single.log file. How do I get the log file?

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