[phenixbb] special positions

Pavel Afonine pafonine at lbl.gov
Wed Jun 18 13:01:37 PDT 2014

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..


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 <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> 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 <pafonine at lbl.gov
>>     <mailto:pafonine at lbl.gov>> 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

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