[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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 " <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





_______________________________________________
modeller_usage mailing list
modeller_usage@salilab.org
https://salilab.org/mailman/listinfo/modeller_usage

_________________________________________________________________
MSN Hotmail is evolving - check out the new Windows Live Mail http://ideas.live.co.uk