Re: [ccp4bb] brute force MR

[Ian Stokes-Rees]

For anyone who is interested, I meant to include a reference to the PNAS paper 
that has just come out (web-only early release) describing the wide search MR 
strategy we've developed:

Stokes-Rees, Sliz
Protein structure determination by exhaustive search of Protein Data Bank 
derived databases
Proc. Nat'l Academy of Sciences
doi:10.1073/pnas.1012095107
http://www.pnas.org/content/early/2010/11/17/1012095107

Ian

Re: [ccp4bb] brute force MR

[Ian Stokes-Rees]

Arnon,

We have developed an MR search mechanism which may be helpful in this scenario. 
 It is web accessible and available to any public or academic researchers:

https://portal.nebiogrid.org/secure/apps/wsmr/

It can use up to the full set of SCOP domains (100k) to attempt a Phaser MR 
placement of each domain and then ranks the results, allowing you to identify a 
single well placed domain.  The web-based system does not allow you to fix that 
domain to continue the search for subsequent domains but we can do this from 
the command line interface.  If you have a particular set of domains you'd like 
to search against (RCSB or SCOP PDB codes), then we can limit the search to 
that set.

If you decide to use this, please contact us once your first domain search has 
been completed (these take 2-3 years of serial computing time and will finish 
in 1-3 days, depending on how many other computations are ahead of it in our 
queue, the complexity/resolution of your data set, space group, and unit cell 
size).

Regards,

Ian Stokes-Rees

Re: [ccp4bb] brute force MR

[Eleanor Dodson]

On 12/07/2010 09:38 PM, Arnon Lavie wrote:

Hi there:

The situation: We are facing difficult molecular replacement: we believe
we have two molecules in the ASU, but phaser/molrep find only one. Using
the electron density calculated using this single molecule, we have
manually placed the 2nd molecule, albeit not good enough for rigid body
refinement.

Our strategy: We are looking for a program to do a 3 dimensional search
around the current position of the 2nd molecule. Maybe one that
calculates R-factor at the different positions, to allow to identify the
correct one. ...

Does anyone know of such a program, or an alternative approach?

Thanks.

Arnon


MOLREP will do this SAPT???..
E

Re: [ccp4bb] brute force MR

[Randy Read]

Hi,

There are a number of possibilities that come to mind:

1. Use the "ROTATE AROUND" option of the brute-force rotation function in 
Phaser to generate a set of rotation angles similar to your real-space 
solution, then use each of these for a full translation search.  

2. Use my old program BEAST to do exactly the limited 6D brute-force search 
that you ask about, in one run.  But this is probably not better or even faster 
than doing the full translation search with the fast methods in Phaser, which 
is why we didn't bother making this kind of search convenient in Phaser.

3. The map around your positioned model should look a bit more like the real 
structure than the model does, so cut out the density (using a mask constructed 
from your coordinates) and search for the second copy in Phaser using that 
density.  This is similar to what we did to solve the angiotensinogen structure 
(supplementary material in Zhou et al, Nature 468, 108-111, 2010).  Cutting out 
density can be a bit tricky, so we describe how to do that on our web page: 
http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model.  
The procedure is still a bit tricky after that, so we're working on automating 
it.  You might want to ask for more advice if you pursue this option.

4. Carry out refinement on the one-molecule solution, then use the refined 
model to search for the second copy.  I think this strategy is part of the 
Balbes pipeline, and we've had some good results with that kind of thing too.

5. Wait a bit, and then some new features in Phenix and Rosetta will be 
available so that you can use Rosetta to rebuild your one-molecule model, 
adding information from the density to the sophisticated energy functions and 
conformational search tools in Rosetta.  I should mention that this is a 
project involving Tom Terwilliger, David Baker and a lot of work by Frank 
DiMaio in David Baker's group.

Regards,

Randy


On 7 Dec 2010, at 21:38, Arnon Lavie wrote:

> Hi there:
> 
> The situation: We are facing difficult molecular replacement: we believe we 
> have two molecules in the ASU, but phaser/molrep find only one. Using the 
> electron density calculated using this single molecule, we have manually 
> placed  the 2nd molecule, albeit not good enough for rigid body refinement.
> 
> Our strategy: We are looking for a program to do a 3 dimensional search 
> around the current position of the 2nd molecule. Maybe one that calculates 
> R-factor at the different positions, to allow to identify the correct one. ...
> 
> Does anyone know of such a program, or an alternative approach?
> 
> Thanks.
> 
> Arnon
> 
> -- 
> ***
> Arnon Lavie, Professor
> Dept. of Biochemistry and Molecular Genetics
> University of Illinois at Chicago
> 900 S. Ashland Ave.
> Molecular Biology Research Building, Room 1108 (M/C 669)
> Chicago, IL 60607
> U.S.A.
> Tel:(312) 355-5029
> Fax:(312) 355-4535
> E-mail: la...@uic.edu
> http://www.uic.edu/labs/lavie/
> ***

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

Re: [ccp4bb] brute force MR

[Anastassis Perrakis]

If the two molecules are related by translational symmetry, at least  
Phaser is not happy.
Since in the second rotation function it removes contribution from the  
first orientation,
if the orientation/rotations of the two molecules in identical, it  
will fail to see the

second rotation applies.

Thus if you have pure translation symmetry, which must be manifested  
with a very high peak

in the native Patterson map, you can either:

1. RTFM of Phaser and supply a list with the first solution and the an  
identical rotation, and ask

it to find the second translation
2. Apply the second translation by hand from the native Patterson (as  
you more or less did empirically)
3. 'Fool' Phaser by telling it you look for two different molecules,  
first the one and then the other.


Tassos

On Dec 7, 2010, at 22:38, Arnon Lavie wrote:


Hi there:

The situation: We are facing difficult molecular replacement: we  
believe
we have two molecules in the ASU, but phaser/molrep find only one.  
Using

the electron density calculated using this single molecule, we have
manually placed  the 2nd molecule, albeit not good enough for rigid  
body

refinement.

Our strategy: We are looking for a program to do a 3 dimensional  
search

around the current position of the 2nd molecule. Maybe one that
calculates R-factor at the different positions, to allow to identify  
the

correct one. ...

Does anyone know of such a program, or an alternative approach?

Thanks.

Arnon

--
***
Arnon Lavie, Professor
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1108 (M/C 669)
Chicago, IL 60607
U.S.A.
 Tel:(312) 355-5029
 Fax:(312) 355-4535
 E-mail: la...@uic.edu
 http://www.uic.edu/labs/lavie/
***


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

Re: [ccp4bb] brute force MR

[Nian Huang]

Try this, assuming you have good data. Use one molecule you got to do
refinement (rigid body or restraint refinement with tight restraint)
and phase the map.  Then do a phased map molecular replacement. You
might want only use the core of your protein to do the molecular
replacement search to avoid the clashing problem. It worked once for
me even the map was very bad.

Nian

On Tue, Dec 7, 2010 at 3:38 PM, Arnon Lavie  wrote:
> Hi there:
>
> The situation: We are facing difficult molecular replacement: we believe we
> have two molecules in the ASU, but phaser/molrep find only one. Using the
> electron density calculated using this single molecule, we have manually
> placed  the 2nd molecule, albeit not good enough for rigid body refinement.
>
> Our strategy: We are looking for a program to do a 3 dimensional search
> around the current position of the 2nd molecule. Maybe one that calculates
> R-factor at the different positions, to allow to identify the correct one.
> ...
>
> Does anyone know of such a program, or an alternative approach?
>
> Thanks.
>
> Arnon
>
> --
> ***
> Arnon Lavie, Professor
> Dept. of Biochemistry and Molecular Genetics
> University of Illinois at Chicago
> 900 S. Ashland Ave.
> Molecular Biology Research Building, Room 1108 (M/C 669)
> Chicago, IL 60607
> U.S.A.
>                             Tel:        (312) 355-5029
>                             Fax:        (312) 355-4535
>                             E-mail:     la...@uic.edu
>                             http://www.uic.edu/labs/lavie/
> ***
>

Re: [ccp4bb] brute force MR

[Bosch, Juergen]

Just a thought:
shave off parts of your model1, which you think might cause a clash perhaps, 
essentially keeping a core in place, then rerun molrep using model1 as fixed 
and search for a second. If you are successful, then SSM superimpose your 
complete model onto both and see what you have to fix the problem.

Jürgen

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.mac.com/bosch_lab/

On Dec 7, 2010, at 4:38 PM, Arnon Lavie wrote:

Hi there:

The situation: We are facing difficult molecular replacement: we believe
we have two molecules in the ASU, but phaser/molrep find only one. Using
the electron density calculated using this single molecule, we have
manually placed  the 2nd molecule, albeit not good enough for rigid body
refinement.

Our strategy: We are looking for a program to do a 3 dimensional search
around the current position of the 2nd molecule. Maybe one that
calculates R-factor at the different positions, to allow to identify the
correct one. ...

Does anyone know of such a program, or an alternative approach?

Thanks.

Arnon

--
***
Arnon Lavie, Professor
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1108 (M/C 669)
Chicago, IL 60607
U.S.A.
 Tel:(312) 355-5029
 Fax:(312) 355-4535
 E-mail: la...@uic.edu
 http://www.uic.edu/labs/lavie/
***

[ccp4bb] brute force MR

[Arnon Lavie]

Hi there:

The situation: We are facing difficult molecular replacement: we believe 
we have two molecules in the ASU, but phaser/molrep find only one. Using 
the electron density calculated using this single molecule, we have 
manually placed  the 2nd molecule, albeit not good enough for rigid body 
refinement.


Our strategy: We are looking for a program to do a 3 dimensional search 
around the current position of the 2nd molecule. Maybe one that 
calculates R-factor at the different positions, to allow to identify the 
correct one. ...


Does anyone know of such a program, or an alternative approach?

Thanks.

Arnon

--
***
Arnon Lavie, Professor
Dept. of Biochemistry and Molecular Genetics
University of Illinois at Chicago
900 S. Ashland Ave.
Molecular Biology Research Building, Room 1108 (M/C 669)
Chicago, IL 60607
U.S.A.
 Tel:(312) 355-5029
 Fax:(312) 355-4535
 E-mail: la...@uic.edu
 http://www.uic.edu/labs/lavie/
***