[phenixbb] ADP restraints - distance power, average power, etc

Ed Pozharski epozh001 at umaryland.edu
Tue Dec 21 08:23:56 PST 2010

I think Joe has figured it out already.  Trying a different program when
the one you are using gives you trouble is a sure way to see if the
problem lies with data (I assume that buster, cns, phenix, refmac and
shelx all produce maps that resemble the same reality, and if positive
density comes from data it will hopefully show up in all cases).  As for
metaphors, it's more like plugging the same video card in two computers
to see if the problem is the card itself or the motherboard.

IIUC, the kick maps are intended to reduce bias and maybe get one a
better density in not-so-clear region.  As far as well refined model
regions go, calculating phases from a set of models with randomly
shifted atoms seems to certain extent resemble increasing the B-factors.
So the positive density that shows up first on the heavier and/or less
disordered atoms seems like an expected outcome.



On Mon, 2010-12-20 at 21:43 -0800, Pavel Afonine wrote:
> > Refine with refmac and see if the positive density shows up there too.
> > If it does, then either there is something peculiar about your structure
> > or both programs suffer from the same bug that somehow only shows up
> > with your particular dataset.  If not, then it is indeed phenix bug
> > (still rather specific to your dataset).
> Although this may definitely give more clues, I see this way of 
> debugging this problem more like treating the appendicitis with Tylenol 
> -:) This may help in some way but will unlikely identify the problem and 
> fix its root. Solving a puzzle like this typically involves reducing the 
> amount of "variables" by simplifying the task that still results in 
> problem rather than making it more complex to solve by involving more 
> "variables". Oh, I guess you know what I mean by "variables" so I don't 
> go into it.
> All the best!
> Pavel.
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

More information about the phenixbb mailing list