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.

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.

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
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Randy J. Read

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