Re: [modeller_usage] How to incorporate NAD and water in my model
To:
Subject: Re: [modeller_usage] How to incorporate NAD and water in my model
From: "Charlie Allerston" <>
Date: Wed, 14 Mar 2007 15:29:00 +0000
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.