Re: [ccp4bb] brute force molecular replacement

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

Previous message:
Subject: Re: brute force molecular replacement
From: Nicholas M Glykos glykos {- at -} MBG {- dot -} DUTH {- dot -} GR
Date: 2009-02-02

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From: Christoph Parthier chris_maillist {- at -} BC {- dot -} BIOCHEMTECH {- dot -} UNI-HALLE {- dot -} DE
Date: 2009-02-02

Subject: Re: brute force molecular replacement
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2009-02-02

Hi -

With good 2.0 A data (as you seem to have) and a correct solution,
I would be rather surprised if ARP/wARP - REFMAC5 would not refine and
build a model without major trouble.
Did you try that at all ?

To be more detailed I would:

0. Put the mol rep solution in ARP/wARP and let it run (in the
meantime proceed to 1-3 if 0. fails ...)
2. Do some density modification using the model phases (if you are in
ccp4 simplest is to use DM)
3. Use the DM phases and pretend this is an 'experimental' solution in
ARP/wARP

More info and ideas are in:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18094467

Note that both ARP/wARP runs above can be done in the web server
without the need of local installation if you prefer.

http://cluster.embl-hamburg.de/ARPwARP/remote-http.html

Apologies for the shameless plug-ins but I really think its the
easiest thing to do, even if it might now work.

Tassos

On Feb 2, 2009, at 10:10, Nicholas M Glykos wrote:

>
> Hi Xie,
>
>> Many thanks to all who responded to my earlier query (Drs. Paul
>> Swepston, Randy Read and Nicholas Glykos). I am trying to determine
>> the
>> structure of a very long coiled coil dimer (roughly 150 residues
>> long)
>> by molecular replacement. I don't know if it forms a canonical coiled
>> coil from end to end (it probably doesn't). I seem to get the right
>> solution using different lengths of polyala (and polygly and modeled
>> ones with side-chains) coiled coils as my search models (maps show
>> some
>> density for unmodeled parts of the coiled coil structure).
>
> If your current best phase-set gives you back correct information
> that was
> not part of your model, you are doing fine. You are getting there
> (but it
> may take a while).
>
> Starting from your current best polyAla model, you can give it a try
> with
> very many runs of torsion angle simulated annealing (starting from a
> high
> temperature), or with rigid-body simulated annealing (both from
> within CNS
> or XPLOR). Don't do positional refinement. With an almost perfect
> polyAla
> model you should expect R-free and R in the low 40s (%) range for ~2A
> data.
>
>
>> However, building a model accounting for the entire sequence, getting
>> the correct chain direction and placing residue side-chains have
>> proved
>> difficult. And my R-facs have never improved beyond the low 50s
>> during
>> different refinement attempts. At the moment, I have 3 more or less
>> contiguous 30 residue stretches of coiled coil found by 3 independent
>> molecular replacement attempts using epmr (This was done to account
>> for
>> possible bends, stutters in the dimer). I am trying to get the rest
>> of
>> the model by new rounds of molecular replacement using epmr. I have
>> carried out exhaustive runs using epmr. But I haven't found the
>> rest of
>> the model. What are the options available to me with molecular
>> replacement? I have tried molrep, phaser and amore from the ccp4
>> suite.
>> My diffraction data is quite good (data between 25 and 2 A with an
>> Rsym
>> of 8%).
>
> I'm not sure whether what you really need is more molecular
> replacement.
> Maybe you should invest more time with the maps (combined with 'safe'
> simulated-annealing-based optimisation methods). What I've just said
> only
> applies if these 90 residues you have can indeed produce correct
> information that was not part of the initial model (as you said).
>
>
>> Can I run Qs when a partial structure is available?
>
> No. Sorry.
>
>
> Nicholas
>
>
> --
>
>
> Dr Nicholas M. Glykos, Department of Molecular
> Biology and Genetics, Democritus University of Thrace,
> University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613
> Tel ++302551030620 (77620), http://www.mbg.duth.gr/~glykos/
>

P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

CCP4bb navigation

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

Previous message:
Subject: Re: brute force molecular replacement
From: Nicholas M Glykos glykos {- at -} MBG {- dot -} DUTH {- dot -} GR
Date: 2009-02-02

Next message:
Subject: UV-transmissible plate seals 96-well format
From: Christoph Parthier chris_maillist {- at -} BC {- dot -} BIOCHEMTECH {- dot -} UNI-HALLE {- dot -} DE
Date: 2009-02-02