- modeller_usage - salilab.org

...disulfide and loops
by Joel Tyndall 09 Nov '09

09 Nov '09

Thanks guys. That's a great help. Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 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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More than one Proline in helix!
by Raghu Bhagavat 09 Nov '09

09 Nov '09

hello.... I modeled a protein using 2 templates in Modeller9...1-312 residues w.r.t one protein and the next 65 resdiues w.r.t another protein....The template selection is done carefully and both the templates share a good homology with my query sequnce.... But, i have got prolines in helix which i doubt about its existence.....Its a pretty long helix in which 3 prolines are present and 2 of them are in the middle of long helix.....There is an immediate loop following this and then another helix having 2 Prolines.... Can anybody suggsest how modeler came up with such a model having Prolines in helix?? Is it valid ?? how stable is it?? has anybody encountered with the same Proline issue with any other protein? Please post in your views......

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Including a Thioester linkage
by João Rodrigues 09 Nov '09

09 Nov '09

Dear All, I'm currently trying to model a protein that has a thioester linkage between two residues. I've searched archives and Google and there's no mention on how to include such a linkage in the model. So the question is: is it possible? If so, how? If not, how can I overcome this? Best regards to all and thanks for the answers, João [ .. ] Rodrigues (Blog) http://doeidoei.wordpress.com (MSN) always_asleep_(a)hotmail.com (Skype) rodrigues.jglm

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loops and disulfide
by Joel Tyndall 09 Nov '09

09 Nov '09

Hi folks, I'm looking to generate a model with a disulfide constraint as well as loop refinement. I am still getting my head around the python scripts. In the old top files, one could do multiple things in the single top file. I can't seem to get past this issue with the python scripts. I can run things separately but I am at a loss trying to combine them. I seem to be stuck with a = loopmodel(env,.... vs a = MyModel (having defined the disulfide patch Could someone help or direct me to the write web page. Is this the process to actually run two separate cripts (generate disulfide then run loop refinement? Many thanks in advance An example script would be awesome J _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034

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Alignment
by SHANG Yuan 09 Nov '09

09 Nov '09

Hi,all. I'm new to Modeller. Since I suspect the align result of "align2d()" function, so I just simple recruited a multiple alignment of a domain family, and then I create the "*.ali" file by hand. But when I try to run "automodel" module, and it indicates "E> Sequence difference between alignment and pdb :". I'm sure my sequence in the alignment and pdb are the same since I have succeeded by using the alignment file created by "align2d()" function. I paste my own alignment below: >P1;myo10fermA structureX:myo10ferm.pdb: 197 :A:+213 :A:::-1.00:-1.00 ---EMTSTVYCHGGGSCKITINSHTTAGEVVEKLIAGLAMADSANMFALFEYNGHVDKAIESR-TVVADVLAKFE KLAATSEVGDLP--WKFYFKLYCFLDTDNVPKDSVEFA-FMFEQAHEAVIHGHHPAP-EENLQVLAALRLQYLQG DYTLH-AAIPPLEEVYSLARLKAR-AAAAEEVS--SARASIIDKWRKF-QGMNQAQAMAKYMALIKEWPGYGSTL F* >P1;myo7f sequence:myo7f: : : : ::: 0.00: 0.00 SKKPIMLPVTFMDGTTKTLLTDSATTARELCNALADKISL-KDRFGFSLYIALFDKVSSLGSGSDHVMDAISQCE QYAKEQGAQERNAPWRLFFRKEVFTPW-HNPSEDNVATNLIYQQVVRGVKFGEYRCEKEDDLAELASQQYFVDYG SEMILE------RLLSLVPTYIPDREITPLKN-LEKWAQLAIAAHKKGIYAQRRTDSQ-KVKEDVVNYARFKWPL L* And the alignment file created by "align2d()":(This works well with automodel) >P1;myo10fermA structureX:myo10ferm.pdb: 197 :A:+213 :A:::-1.00:-1.00 ---EMTSTVYCHGGGSCKITINSHTTAGEVVEKLIAGLAMADSANMFALFEYNGHVDKAIESRTVVADVLAKFEK LAATSEV--GDLPWKFYFKLYCFLDTDNVPKDSVEFAFMFEQAHEAVIHGHHP-APEENLQVLAALRLQYLQGDY TLHAAIPPLEEVYSLARLKAR/A/AAAEEVSSARASIIDKWRKFQGMNQAQAMAKYMALIKEWPGYGSTLF* >P1;myo7f sequence:myo7f: : : : ::: 0.00: 0.00 SKKPIMLPVTFMDGTTKTLLTDSATTARELCNALADKISLKDRFGFSLYIALFDKVSSLGSGSDHVMDAISQCEQ YAKEQGAQERNAPWRLFFRKEVFTPWHNPSEDNVATNLIYQQVVRGVKFGEYRCEKEDDLAELASQQYFVDYGSE MILERLLSLVPTYIPDREITP-L-KNLEKWAQLAIAAHKKGIYAQRRTDSQKVKE--DVVN-YARFKWPLL* Any advice will be welcome.and Thanks in advance. Yuan SHANG

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Selection criteria for building sequence database - pdball.pir
by Praveen Raj 05 Nov '09

05 Nov '09

Hi, I'm trying to rebuild the pdball.pir file from a set of pdb files, using the model.make_chain() as mentioned in modeller website and I noticed certain filter criteria as parameters to make_chain() such as minimal_chain_length=30 minimal_stdres=30 chop_nonstd_terminii=True max_nonstdres=10 minimal_resolution=99.0 structure_types='structureN structureX' And while processing I found that certain pdb files are skipped due to this filter criteria. My query is 1) Are these the standard criteria for building pir file? 2) Or adjusting the values to 0 (except min. res) will alter the purpose ? Thanks for any help Praveen Raj

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Re: [modeller_usage] Including a Thioester linkage
by João Rodrigues 04 Nov '09

04 Nov '09

Thanks for the tip Joel. I think I found what I need: here<http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/force…> I did a small search in the modlib folder and I couldn't find anything like this so I assume I'll have to add it myself. Any idea how I load this topology to my script? Regards! João [ .. ] Rodrigues (Blog) http://doeidoei.wordpress.com (MSN) always_asleep_(a)hotmail.com (Skype) rodrigues.jglm I’m guessing a patch residue will be what you need. Unfortunately Idon’t > know how to write them. Check out the manual for a patch. > > > > J > > > > _________________________________ > > Joel Tyndall, PhD > > Senior Lecturer in Medicinal Chemistry > National School of Pharmacy > University of Otago > PO Box 56 Dunedin 9054 > New Zealand > http://www.researcherid.com/rid/C-2803-2008 > > Pukeka Matua > Te Kura Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 56 Otepoti 9054 > Aotearoa > > Ph / Waea +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 >

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Disulfide
by Joel Tyndall 04 Nov '09

04 Nov '09

Hi there, I am building relatively simple models and I have added in my own DISU patch as per the recommended method via FAQ. The disulfide is formed but the dihedrals don't look correct (~150 degrees). Is there something I am missing? (Do I need to add in a larger refinement factor? I am using mod9v7 Cheers Joel Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 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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Tutorial, Advanced example
by Marco 03 Nov '09

03 Nov '09

Hi, I still have a question on the Tutorial. In the Advanced example some news structures are used to improve the model using multiple alignment. But some of this, like 1b8p, are already present in the Basic example and discarded...This is not very clear, at least for me.... :-) Thanks for your help, Marco

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Modeling ligands in the binding site
by Qinghua Liao 03 Nov '09

03 Nov '09

Hi Modeller users, I have a problem of Modeling ligands in the binding site, I have read the manual online, but I still can't understand exactly! my question is what the differences of alignment between that of with and without ligand! Is it just the value of env.io.hetatm? And how to set the atoms with restraint? Could somebody share the all python scripts used during the entire process of Modeling ligands in the binding site? Any response will be highly appreciated! All the best, Qinghua Liao

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