[ccp4bb] Low resolution chain tracing

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: CCP4 - Monomer library sketecher
From: Sridhar Prasad SridharP {- at -} MBASIS {- dot -} COM
Date: 2007-06-15

Next message:
Subject: Re: Low resolution chain tracing
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-06-15

Subject: Low resolution chain tracing
From: Alexei Datsuk alexeidatsuk {- at -} GMAIL {- dot -} COM
Date: 2007-06-15

Hi,

I need some advice from experts. I have a low resolution electron density
map (3.7 angstroms) solved by SIRAS. The protein is a tetramer (47
kDa/monomer) but I'm having trouble getting in register. There is very good
main chain density and clear secondary structure (beta-sheets) so I likely
have solved it correctly. I can trace most of the main chain as fragments
(loops connecting beta strands are broken) but I can't tell if I'm tracing
it in the right direction or whether I have it backwards. There is no real
density for side chains at all (except for Calpha), not even aromatics, so I
have no clue which way is N or C-terminus. There are a few disulfide bonds
too so I'm real worried about tracing incorrectly and never being able to
fix it later. My strategy right now is to build in as much poly-ala
fragments (I can get ~75% of trace as fragments) and then refine them. Then
redo phasing in SHARP with poly-ala model and SIRAS phases and then use DM
with NCS averaging to get improved map. Hopefully I can see then side chain
density. My question is how much bias would be incorporated if some of the
fragments are traced backwards? Would I be able to sort things out if some
fragments are traced backwards? Has anyone traced chains as fragments not
knowing which direction is which and then be able to sort things out later?
Right now I am stuck- I have spent the last 1 months trying to get things in
register but no luck. I don't want to build haphazardly but it doesn't look
like I have much choice.

What have people done when tracing in low resolution maps?

Thanks

Alexei

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: CCP4 - Monomer library sketecher
From: Sridhar Prasad SridharP {- at -} MBASIS {- dot -} COM
Date: 2007-06-15

Next message:
Subject: Re: Low resolution chain tracing
From: "Das, Debanu" debanu {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2007-06-15