Re: [ccp4bb] Low resolution chain tracing

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

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

Next message:
Subject: Fw: conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
From: deliang chen deliangc {- at -} UCI {- dot -} EDU
Date: 2007-06-15

Subject: Re: Low resolution chain tracing
From: Jeff Lee jlee {- at -} SCRIPPS {- dot -} EDU
Date: 2007-06-15

Hi,

Ah yes, low resolution chain tracing.... I'm only in the initial
stages of map interpretation, but I anticipate I might have a similar
problem. I would love to hear from anyone who has ideas as well.

Thanks

Jeff

On Jun 15, 2007, at 10:03 AM, Alexei Datsuk wrote:

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

Next message:
Subject: Fw: conversion of .fcf to 2fo-fc.map and fo-fc.map of ccp4 format
From: deliang chen deliangc {- at -} UCI {- dot -} EDU
Date: 2007-06-15