[phenixbb] special positions

[Pavel Afonine]

Hi Yarrow,

I guess it this point it's easiest of you send me files and I try 
various things myself. Then I send you what I get and also post summary. 
Of course all files will be handled confidentially! I may not be able to 
look into this right away but I wil do my best to look by tonight.

Pavel

On 6/18/14, 1:25 PM, Yarrow Madrona wrote:
> Hi Pavel,
>
> The waters move away when I do as you suggested. I am providing a 
> screen shot:
>
> https://www.dropbox.com/s/lv1vvq8kcr8rion/special_positions_2.png
>
> I'm not sure what is going on but there is definitely a 2 fold 
> symmetry near these waters.
>
> -Yarrow
>
>
> On Wed, Jun 18, 2014 at 1:01 PM, Pavel Afonine <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> wrote:
>
>     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 <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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