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Re: [modeller_usage] How to incorporate NAD and water in my model



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 " <>
Reply-To: deepti  <>
To: 
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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