Hi Yarrow,

if you are at the water picking stage then it's almost certain you don't need to do rigid-body refinement. Normally, you do rigid-body refinement once at the very beginning if you believe it's necessary. Regarding that water. What happens if you run refinement without rigid-body and with automatic water update (that will add/remove/refine waters)?

Here is how phenix.refine treats atoms on special positions. It it "sees" an atom close to special position (within some tolerance, which is 0.5 or 1A, I forgot exact number) it moves that atoms exactly onto special position, and then keep it there throughout refinement. So if you see that water moves, then I guess it is close to s.p. but not enough. Or perhaps there is something else is going on..

Pavel

On 6/18/14, 12:06 PM, Yarrow Madrona wrote:
Hi Pavel,

It turns out I do have some special positions. Waters sit near a 2 fold axis. I have given them 0.5 occupancy. No error comes up but they simply get kicked out of the electron density. Maybe I should turn off rigid body refinement since I don't need it? Below is a link to a screen shot.

https://www.dropbox.com/s/lt3hqzjmygin9l8/special_position.png


On Wed, Jun 18, 2014 at 8:49 AM, Pavel Afonine <[email protected]> wrote:
Hi Yarrow,

oh good! I'm glad you solved the problem -:)

All the best,
Pavel


On 6/18/14, 8:02 AM, Yarrow Madrona wrote:
Hi Pavel,

Thanks for your quick response. It turns out that after I reprocessed a data set in a higher symetry space group I forgot to use a reference mtz so the orientation was completely off. I just re-ran phaser and everything worked fine. I didn't run rigid body refinement after phaser.

The original error message didn't list the atoms and I am not sure how it could have any atoms on special positions with the solution being completely wrong. Probably nothing to worry about.

-Yarrow

On Tuesday, June 17, 2014, Pavel Afonine <[email protected]> wrote:
Hi Yarrow,

ok, I wish that error message (that I put a while ago, in 2009 to be precise) lists those atoms... Can you send me the file so I can tell you what these atoms are?

In general, if at rigid-body refinement stage you have atoms at special positions it is unlikely to be right.

Pavel

On 6/17/14, 12:56 PM, Yarrow Madrona wrote:
Hi,

I am trying to do rigid body refinement, however I get an error in phenix telling me that there are atoms at special positions.

I am not sure how to determine which atoms are at special positions so that I can exclude them from rigid body refinement. Can someone help me with this? Thank you.

-Yarrow