[phenixbb] fixing a partial solution of mol. rep.

Randy Read rjr27 at cam.ac.uk
Mon Nov 24 02:10:50 PST 2008

Hi Maia,

If you're running AutoMR from the command-line wizard, you can specify  
fixed components with the various fixed_* variables.  You can find an  
example for fixing beta-lactamase and searching for BLIP in the  
documentation (http://www.phenix-online.org/documentation/ 
automr.htm).  It's possible to specify that you have six fixed  
components (for the six copies of the monomers making up the core  
hexamer), but it might be easier to specify a "core" ensemble  
containing the partial solution for the core hexamer, and then specify  
it as a fixed ensemble with orientation angles and translation vector  
both of  0,0,0.

You can also do this in the AutoMR wizard run as a GUI, by choosing  
the various fixed_* variables in the "Choose variable to set" pulldown.

The third option (though this may not be the right forum to mention  
it!) is to run Phaser from the ccp4i interface.  AutoMR is much easier  
for more straightforward problems, but the ccp4i interface is still  
more flexible for getting at advanced features of Phaser in difficult  
cases.  We're working to improve the Phenix interface for the next  
release of Phenix.  Anyway, in the ccp4i interface, you just provide  
a .sol file containing the 6 SOLU 6DIM... lines defining the core  
hexamer as a fixed partial solution, then tell Phaser to look for  
copies of the other monomer.

In a difficult case like this, it's possible that one or two of the  
copies of the second component will give a clear solution, which would  
show the relationship between the monomers in the core and monomers of  
the second molecule.  Then you could try solving the structure by  
making an alpha+beta object (where alpha is a monomer in the core, and  
beta is the second type of monomer) and looking for six copies of  
that, or superimpose copies of the alpha+beta object on copies of  
alpha still lacking a companion.

Good luck!


On 24 Nov 2008, at 00:33, chern wrote:

> I am doing a molecular replacement.
> There are two types of protein molecules in the crystal. One type is  
> forming a hexameric core; there are 6 molecules of the second type  
> that I need to locate.
> I found a solution for the hexameric core, but the other 6 molecules  
> are difficult to find.
> 1. Can I fix the solution for the core, so that I don't have to find  
> it every time. The other inconvenience with that is that the origine  
> is different for every new run. If I fix the hexamer, then I fix the  
> origine. It's important to me to compare different runs of MR.
> 2. Some of the six other molecules that MR finds are not the closest  
> to the core. How can I request to output the closest molecules?
> Maia
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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 Road                                    E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                       www- 

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