Re: [ccp4bb] SFALL problem - weird atom maps

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

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Subject: Re: Fedora core 6 install problem
From: Flip Hoedemaeker flip {- at -} KEYDP {- dot -} COM
Date: 2007-06-25

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From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-06-25

Subject: Re: SFALL problem - weird atom maps
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-06-25

I understand this surprising feature now ..

The atomic density is being smeared by the BADD 100 to cover a volume >
3A from the atomic centre. (3.2A to be more precise..)

But the limit on the map sections to be included in the inverse fft is
calculated without that BADD - in fact you use the default 2.5A.

This means that an atom on the first section (y=0.0) does not include
the density in sections y=-2.5/NY to -3.2/NY
Hence the peculiarity.

It goes away if you move the atom to (x,y,z) = (0,3,0)

Will try to fix sfall, but for the time being either do not use BADD ,
or move the atom..
Eleanor

Stefano TRAPANI wrote:
> 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:

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

Previous message:
Subject: Re: Fedora core 6 install problem
From: Flip Hoedemaeker flip {- at -} KEYDP {- dot -} COM
Date: 2007-06-25

Next message:
Subject: Re: Fedora core 6 install problem
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-06-25