Do you have to use the modeller alignment script? I have been using ebi software to create a .pir file.
After reading the modeller files and tutorials i am still at a loss as to how to use these 'blk' characters. I am trying to get a molecule of fad that is present in my template into my model.
>From: Joel Tyndall joel.tyndall@otago.ac.nz >To: deepti s_pinkbutterfly@rediffmail.com, modeller_usage@salilab.org >Subject: Re: [modeller_usage] How to incorporate NAD and water in my model >Date: Thu, 15 Mar 2007 11:27:59 +1300 > > >Hi Deepti, > >I recently looked at a similar complex that included ATP and Mg. You can >add a # to your alignment file for NAD. See the response to my post >below (just replace ATP with NAD). > >Cheers > >J > >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 > > >deepti wrote: > > > > > > Dear Modeller caretakers, > > I am trying to construct a model for a protein having a known > > structure for the purpose of learning Modeller. > > The pdb structureis in form of protein-NAD adduct. My aim is to build > > a similar model. > > Using the templates I have built a model, please tell me how to > > incorporate NAD and water in my model. I have read the manual 'faq' , > > but am confused how to change my alignment (including '.' for BLK > > residues and 'w' ). How do I change the template pdb files for this? > > How do I make my own restraint file? > > My alignment file is(generated by align2d.py):- > > > > >P1;1qsgA > > structureX:1QSG.pdb: 2 :A: 259 :A:undefined:undefined:-1.00:-1.00 > > >GFLS-GKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQND--KLKGRVEEFAAQLGSDIVLQCDVAEDASIDT > > >MFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIAHDISSYSFVAMAKACRSMLNPGSALLTLSYLG > > > > >AERAIPNYNVMGLAKASLEANVRYMANAMGPEGVRVNAISAGPIRTLAASGIK--------DFRKMLAHCEAVTP > > IRRTVTIEDVGNSAAFLCSDLSAGISGEVVHVDGGFSIAAMNEL* > > > > >P1;1eny > > sequence:1eny: : : : ::: 0.00: 0.00 > > >AGLLDGKRILVSGIITDSSIAFHIARVAQEQGAQLVLTGFDRLRLIQRITDRLPAKAPLLELDVQNEEHLASLAG > > >RVTEAIGAGNKLDGVVHSIGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKALLPIMNPGGSIVGMDFDP > > >S-RAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQR > > APIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL* > > > > > > > > > > I got a lesser objective function while using the alignment generated > > by clustalw. Which would be a better option? > > Also please suggest me ways to further refine my model so as to make > > it almost like the pdb structure. > > > > > > Thanks and Regards, > > Deepti > > > > > > > > dreams > > >http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/1050715198@Middle5/1120029_1114336/1119254/1?PARTNER=3&OAS_QUERY=null%20target=new%20 > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage@salilab.org > > https://salilab.org/mailman/listinfo/modeller_usage > > > >-- >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 > > >_______________________________________________ >modeller_usage mailing list >modeller_usage@salilab.org >https://salilab.org/mailman/listinfo/modeller_usage
_________________________________________________________________ Txt a lot? Get Messenger FREE on your mobile. https://livemessenger.mobile.uk.msn.com/