Stretched Maps

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occupancy refinement of a metal ion

Joel Weadge

20 Oct 2010 20 Oct '10

6:58 p.m.

Hi all,I have just finished doing molecular replacement and an initial round of refinement (with simulated annealing) on a number of different datasets. They have all be straightforward since most of them are either point mutants and/or co-crystal structures. However, two of the structures are giving me some trouble. The data appears to be of good quality and resolution (2.25 and 2.55Å). The MR proceeds as normal with good scores and then in the subsequent round of refinement the maps (2Fo-Fc and Fo-Fc) look strange. The density is stretched or flattened in one direction. Can anyone help me with what I may be overlooking?Thanks in advanceJW

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Nathaniel Echols

20 Oct 20 Oct

7:03 p.m.

On Wed, Oct 20, 2010 at 11:58 AM, Joel Weadge wrote:

...

I have just finished doing molecular replacement and an initial round of refinement (with simulated annealing) on a number of different datasets. They have all be straightforward since most of them are either point mutants and/or co-crystal structures. However, two of the structures are giving me some trouble. The data appears to be of good quality and resolution (2.25 and 2.55Å). The MR proceeds as normal with good scores and then in the subsequent round of refinement the maps (2Fo-Fc and Fo-Fc) look strange. The density is stretched or flattened in one direction. Can anyone help me with what I may be overlooking?

Since our list server rejected Joel's Coot screen capture, I've posted it here: http://cci.lbl.gov/~nat/img/stretched.png My semi-informed guess would be either severe anisotropy or systematic incompleteness (i.e. didn't collect enough degrees). -Nat

Bryan Lepore

7:07 p.m.

check pdb<->mtz mismatch among CRYST1, scale, origin, symmetry, etc.?

Francois Berenger

21 Oct 21 Oct

2:18 a.m.

Nathaniel Echols wrote:

...

On Wed, Oct 20, 2010 at 11:58 AM, Joel Weadge wrote:

...
I have just finished doing molecular replacement and an initial round of refinement (with simulated annealing) on a number of different datasets. They have all be straightforward since most of them are either point mutants and/or co-crystal structures. However, two of the structures are giving me some trouble. The data appears to be of good quality and resolution (2.25 and 2.55Å). The MR proceeds as normal with good scores and then in the subsequent round of refinement the maps (2Fo-Fc and Fo-Fc) look strange. The density is stretched or flattened in one direction. Can anyone help me with what I may be overlooking?

Since our list server rejected Joel's Coot screen capture, I've posted it here:

http://cci.lbl.gov/~nat/img/stretched.png

The picture reminds me the time when I tried to compute a map from a PDB (I think using FFT from CCP4), but the parameters for the grid were wrong. The map looked a little like this after (on one axis it looked like it was "compressed" by some force). But, I really know nothing about crystallography so my experience is probably not relevant. Regards, Francois.

Pavel Afonine

20 Oct 20 Oct

7:33 p.m.

Hi Joel, it used to be the known issue for some rare cases until I fixed it a few months ago. So: 1) could you please try the latest PHENIX from nightly builds and see if you still have this problem: http://www.phenix-online.org/download/nightly_builds.cgi 2) if you still have this problem even using the latest PHENIX, then please send me the data and model (and, optionally the command you used that lead to these maps) and I will investigate. Pavel. On 10/20/10 11:58 AM, Joel Weadge wrote:

...

Hi all,

I have just finished doing molecular replacement and an initial round of refinement (with simulated annealing) on a number of different datasets. They have all be straightforward since most of them are either point mutants and/or co-crystal structures. However, two of the structures are giving me some trouble. The data appears to be of good quality and resolution (2.25 and 2.55Å). The MR proceeds as normal with good scores and then in the subsequent round of refinement the maps (2Fo-Fc and Fo-Fc) look strange. The density is stretched or flattened in one direction. Can anyone help me with what I may be overlooking?

Thanks in advance JW

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Bryan Lepore
Francois Berenger
Joel Weadge
Nathaniel Echols
Pavel Afonine