[phenixbb] special positions

[Yarrow Madrona]

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> 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> 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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