Re: [phenixbb] Question about scale of ED maps from phenix vs map coeffs when displayed in COOT
For phenix maps: the sum is over the entire unit cell. Ralf
Is the sum over the asymmetric unit or the portion of space that happened to be covered by the map? The result of this calculation depends greatly on the amount of solvent region that is included in the sum.
Dale Tronrud
Ralf W. Grosse-Kunstleve wrote:
That was (and is) always a mystery for me: when I look at two maps (both coming from phenix.refine): - one is computed in COOT from phenix.refine map coefficients, and - another one displayed in PyMol using X-plor formatted map.
To make both maps looking identical I have to draw them at different sigma levels, sometime very different. This is true for both fo-fc and 2fo-fc maps.
I have some ideas but no any proofs so I don't want to put my speculations to the bb. So, I have no answer... May be Ralf or Paul E...?
Our "sigmas scaled maps" are simply divided by the "biased standard deviation":
sqrt(sum((value-mean)**2) / n)
The mean of our maps is usually zero, as we don't usually include F000.
Ralf
Hi Dale, this was one of my suspicions... Since Coot computes maps dynamically in a box around the point you click on, I was thinking that it normalizes the map in that box and not in whole unit cell, therefore the difference. I don't know, just a guess. It would be helpful if Paul E. could comment on this... Pavel. On 3/21/09 8:11 PM, Ralf W. Grosse-Kunstleve wrote:
For phenix maps: the sum is over the entire unit cell. Ralf
Is the sum over the asymmetric unit or the portion of space that happened to be covered by the map? The result of this calculation depends greatly on the amount of solvent region that is included in the sum.
Dale Tronrud
Ralf W. Grosse-Kunstleve wrote:
That was (and is) always a mystery for me: when I look at two maps (both coming from phenix.refine): - one is computed in COOT from phenix.refine map coefficients, and - another one displayed in PyMol using X-plor formatted map.
To make both maps looking identical I have to draw them at different sigma levels, sometime very different. This is true for both fo-fc and 2fo-fc maps.
I have some ideas but no any proofs so I don't want to put my speculations to the bb. So, I have no answer... May be Ralf or Paul E...?
Our "sigmas scaled maps" are simply divided by the "biased standard deviation":
sqrt(sum((value-mean)**2) / n)
The mean of our maps is usually zero, as we don't usually include F000.
Ralf
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Hi all, I have a Ca2+ ion in a special position. the ocupancy should be 0.5, as the other half belongs to a symmetry-related molecule. However, refinement makes the occupansy 1. What should I do to prevent this? Should not it find automatically that? Maia
participants (3)
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chern -
Pavel Afonine -
Ralf W. Grosse-Kunstleve