You are not the only one Deepti. After reading the manual and receiving advice I am still no further forward. A step by step instruction on how to incoroporate these blk characters to a model would be useful. Does anyone have any links?
regards
>From: "deepti " s_pinkbutterfly@rediffmail.com >Reply-To: deepti s_pinkbutterfly@rediffmail.com >To: modeller_usage@salilab.org >Subject: [modeller_usage] How to incorporate NAD and water in my model >Date: 14 Mar 2007 13:58:35 -0000 > > 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 > >
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