[phenixbb] special positions
Pavel Afonine
pafonine at lbl.gov
Wed Jun 18 13:30:32 PDT 2014
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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