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Re: [ccp4bb] how to bring back the missing density for half of the structure
 

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CCP4bb <-- 2007 <-- August 2007 <-- 01 August 2007
Previous message:
Subject: Re: how to bring back the missing density for half of the structure
From: Eric Liu supererictaoranliu {- at -} GMAIL {- dot -} COM
Date: 2007-08-01 		Next message:
Subject: PDB format survey?
From: Joe Krahn krahn {- at -} NIEHS {- dot -} NIH {- dot -} GOV
Date: 2007-08-01


Subject: Re: how to bring back the missing density for half of the structure
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2007-08-01

On 1 Aug 2007, at 22:55, Eric Liu wrote:

> Hi All,
>
> Here are the summary from all the answers to my questions:
>
> 1. Try use arp/warp to build the missing part of structure.

I have to clarify to avoid misunderstandings, that :

1. ARP/wARP autotracing is a bad way for building difficult parts
2. The maps from ARP/wARP however can sometimes be better than normal
maps for difficult parts
3. The new ARP/wARP 'Loop building' module can be useful for building
missing loops but not N- and C-termini for now,
and should be a considered a beta version for experimenting.

Tassos

> 2. Build as much as possible for the missing part and the current c-
> terminal domain, using as low as 0.5 contour of the 2Fo-Fc density.
> Generate mask and then do averaging and density modification using
> DM/Resolev/pirate/buccaneer.
> 3. Align the c-terminal part of other closest kinases to the
> current model, then try to find which N-terminal domain matches the
> difference density the best by eyeballing.
> 4. Look into the possiblity of twinning
>
> Thanks,
>
> Eric
>
> On 7/31/07, Eric Liu wrote:
> Hi All,
> I would like to get some help from here for a data set I recently
> worked on. I have been working on a new kinase data set which does
> not have a close homolog. The data was collected to 2.1A
> resolution in space group P212121 however the difference between a
> and b is only 0.5A. If I index the data as P4, Rmerge is increased
> from 13% to 39%. I used the most close homologs which have about
> 37% sequence identity as search model for molecular replacement and
> it seemed I have got the solution by using Phaser with only the c-
> terminal part of the search model and also a long loop removed.
> After changed the different residues back to the target protein,
> the structure was refined to Rfree/R 46% and 43% to 2.1 A
> resolution. The existing c-terminal structure has well defined
> density except 25ish residue at the very c-terminal end doesn't
> have well connected density. Current model contains about 50% of
> overall target residues. I can see some extented difference density
> for several residues going to the N-terminal part and also extented
> density for the C-terminal loop for several residues. I also see
> tones of not well-conncted difference density in the N-terminal
> region. There was no sever clashes between molecules after mount
> all symmetry related molecules. My question is the following:
>
> 1. Have I got the correct solution for the molecular replacement?
> 2. How can I bring back the missing density for the N-terminal
> residues and the loop region?
>
> I would really appreciate any inputs or suggestions.
>
> Eric
>


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CCP4bb <-- 2007 <-- August 2007 <-- 01 August 2007
Previous message:
Subject: Re: how to bring back the missing density for half of the structure
From: Eric Liu supererictaoranliu {- at -} GMAIL {- dot -} COM
Date: 2007-08-01 		Next message:
Subject: PDB format survey?
From: Joe Krahn krahn {- at -} NIEHS {- dot -} NIH {- dot -} GOV
Date: 2007-08-01


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