[phenixbb] Detrmining pixel size

Keller, Jacob kellerj at janelia.hhmi.org
Sun Jul 8 15:25:30 PDT 2018

Hi All,

I agree that this could be a problem, and it seems to be exactly similar to having inaccurate cell constants in crystallography. On both of these issues, I have wondered why not add these parameters to refinement as simple scale factors, even as an independent refinement step, since it's only three parameters? I have heard that it doesn't matter too much bottom line, but I would think it might matter in certain circumstances. The scale factors xyz would just be optimized to make the center of the observed bond length distribution equivalent to the dictionary one. Would be really easy to implement, I would think.


Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004

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-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Reza Khayat
Sent: Sunday, July 8, 2018 4:38 PM
To: Pavel Afonine <pafonine at lbl.gov>; anaa2 <anaa2 at mrc-mbu.cam.ac.uk>
Cc: phenixbb at phenix-online.org
Subject: Re: [phenixbb] Detrmining pixel size


A 1.38Å vs 1.40Å pixel size will make a tremendous difference for complexes like viruses.  Imagine an image reconstruction of a virus that is 200 pixels in diameter -pixels are an EM's readout, not distances.  At 1.38Å/pixel this is a diameter of 276Å, but at 1.40Å/pixel this is a diameter of 280Å.  A 2Å expansion is certainly biologically important.  So an incorrect pixel size of 0.02Å will give the perception that a biologically important phenomenon has occurred.  Thus, despite acceptable refinement statistics one can make incorrect conclusions based on incorrect pixel size.  I'm dealing with this problem when comparing my image reconstructions from different scope to crystal structures. 

This problem is amplified as the virus size increases. 

Best wishes,

Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031

From: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> on behalf of Pavel Afonine <pafonine at lbl.gov>
Sent: Sunday, July 8, 2018 3:59 PM
To: anaa2; PHENIX user mailing list
Subject: Re: [phenixbb] Detrmining pixel size

Hi Noor,

> Does anyone know how to accurately determine the voxel size of an EM 
> map? If you are slightly off (i.e. 1.38 compared to 1.40 pixel) does 
> this affect real space refinement in PHENIX?

if it's not too much off then I would not expect much difference in results except map-model correlation (CC) may be worse.. This is because phenix.real_space_refine works such that no matter what fit to the map is the model geometry must stay within acceptable limits.


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