[phenixbb] special positions
pafonine at lbl.gov
Wed Jun 18 13:01:37 PDT 2014
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.
> 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,
> 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.
>> 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.
>> On 6/17/14, 12:56 PM, Yarrow Madrona wrote:
>> 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.
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