[ccp4bb] SFALL problem - weird atom maps

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Jeroen Mesters mesters {- at -} BIOCHEM {- dot -} UNI-LUEBECK {- dot -} DE
Date: 2007-06-25

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Subject: SUMMARY: questions about hydrophobic core
From: Sebastiano Pasqualato sebastiano {- dot -} pasqualato {- at -} IFOM-IEO-CAMPUS {- dot -} IT
Date: 2007-06-25

Subject: SFALL problem - weird atom maps
From: Stefano TRAPANI stefano {- dot -} trapani {- at -} IBS {- dot -} FR
Date: 2007-06-25

Dear CCP4ers

I got some strange output maps from sfall while I was trying to generate
electron density models for a viral particle using its atomic coordinates.
I systematically observe an unrealistic equatorial valley in the
caculated electron density map:

PippoVirus.png

I made sure that this feature is not due to the graphics programme used
to display the map.
Also, the valley always appears in the xy plane, independent of the
orientation of the atomic model.

In order to understand if I was doing something wrong, I played a bit
with the sfall parameters.
I ended up calculating a rather fine electron density grid for a single
atom placed at the origin (see the attached script and log files).
In the output map, which covers one unit cell, the calcuated density
appears truncated along the y-axis (see the attached 1-sigma contour
plot; the y-axis is the vertical one).
Can anybody explain me that?
Thank you

atom map

--

--------------------------------------------------
Stefano Trapani, PhD

Laboratoire de Microscopie Électronique Structurale
Institut de Biologie Structurale (IBS) J.P. Ebel
UMR 5075, CNRS
41, rue Jules Horowitz
F-38027 GRENOBLE Cedex 1

phones: (from France: replace ++33 with 0)
++33 4 3878.9262
FAX: ++33 4 3878.5494

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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: stereo, dual head, CRT and TFT, Xorg.config, linux
From: Jeroen Mesters mesters {- at -} BIOCHEM {- dot -} UNI-LUEBECK {- dot -} DE
Date: 2007-06-25

Next message:
Subject: SUMMARY: questions about hydrophobic core
From: Sebastiano Pasqualato sebastiano {- dot -} pasqualato {- at -} IFOM-IEO-CAMPUS {- dot -} IT
Date: 2007-06-25