[phenixbb] special positions

[Yarrow Madrona]

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

-Yarrow



On Wed, Jun 18, 2014 at 8:49 AM, Pavel Afonine <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> 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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