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[ccp4bb] questions related to refmac refinement and map-fitting
 

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CCP4bb <-- 2007 <-- March 2007 <-- 19 March 2007
Previous message:
Subject: Re: Can't choose full H-M symbol for conventional cell ?
From: Petrus H Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2007-03-18 		Next message:
Subject: Re: questions related to refmac refinement and map-fitting
From: Lari Lehtio lari {- dot -} lehtio {- at -} KI {- dot -} SE
Date: 2007-03-19


Subject: questions related to refmac refinement and map-fitting
From: lithomas lithomas {- at -} DRAGON {- dot -} NCHU {- dot -} EDU {- dot -} TW
Date: 2007-03-19
Hello,
I am not sure if I can clearly explain the problem , but ..

The protein structure that I tried to solve is 407 a.a. in length. The crystal diffracts to 1.9 Ang and there is one molecule per asym unit. The program that I used is Molrep. Currently I have put in most of the residues and the R is 22.8% and the Rfree is 28.7% (no water added yet) after refmac (v. 5.2) refinement.

I had a hard time trying to finish the refinemnt task because I noticed about ten residues' sidechains persistently had negative density. Typically what I would do is to put these a.a. back to ala and re-check the delFWT map in the next refinement cycle. However, the refmac delFWT map in the next refinement cycle would show strong positive (at least 2.5sigma) values. These amino acids don't seem to have alternate conformations and the Rfactor increase <1% and Rfree increase by 1%. Now, I seems to fall into this trap of endless loop and trying to find a way out.

Since this is the first time that I used refmac, I am not sure if I did something wrong. Everything seems quite straightfoward from the pull-down menu and a couple main parameters that I selected are "restraint refinement", "no prior phase information", "anisotropic" and "babinet scaling". I also tried CNS (v. 1.1) and the results are pretty much the same.

I know I should not let these residues bearing a large blob of negative density on the very end of the side chains. But did anyone have similar probelm and how to resolve this?

Thanks for the help.

Thomas

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 19 March 2007
Previous message:
Subject: Re: Can't choose full H-M symbol for conventional cell ?
From: Petrus H Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2007-03-18 		Next message:
Subject: Re: questions related to refmac refinement and map-fitting
From: Lari Lehtio lari {- dot -} lehtio {- at -} KI {- dot -} SE
Date: 2007-03-19


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