[phenixbb] Phaser with fixed solution

Nathaniel Echols nechols at lbl.gov
Wed Jan 30 09:35:38 PST 2013

On Wed, Jan 30, 2013 at 9:21 AM, Ursula Schulze-Gahmen
<uschulze-gahmen at lbl.gov> wrote:
> I am trying to solve a structure by molecular replacement  in phaser using 2
> model fragments. I think I may have placed the 1st fragment correctly. I
> don't quite understand how to best proceed with a fixed ensemble searching
> for the second fragment in phaser-MR. If I select "use partial solution from
> previous job", do I still need to read in the coordinates of that previous
> solution for one ensemble? And If I do, should I read in the starting
> coordinates or the placed output from this 1st molecular replacement?

I think there are two ways to do it:

1. Use the previous solution, but input the original ensemble (with
the same ID).  This works because that solution has the matrices to
place the ensemble correctly - if you input the model from MR, these
will no longer be valid.

2. Instead of re-using the previous solution, input the placed model,
and check the box "Ensemble is fixed partial solution", which tells
Phaser to simply accept it as-is.

I believe in either case you do not need to specify a separate search
for the already placed component, but I'm not positive about (2).

> The second question is about how to relax the restraints fr the packing. In
> the "other settings" sub window is a section for packing. Could someone
> explain to me what the different options in this packing section mean? Which
> of them should I change to allow for more close contacts?

Partial explanation here:


(hopefully it will be reasonably clear which options in Phenix
correspond to the listed keywords...)


More information about the phenixbb mailing list