Re: [ccp4bb] Modeling residues with very poor density

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

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From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2008-12-11

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Subject: Re: Modeling residues with very poor density
From: Ed Pozharski epozh001 {- at -} UMARYLAND {- dot -} EDU
Date: 2008-12-11

On Tue, 2008-12-09 at 09:31 +0100, Tim Gruene wrote:
> ...you must set the occupancy of those residues to
> zero...

I think this approach (which Tim is not supporting) makes no sense.
When I place an ATOM record into a pdb-file, what I am really saying is
"based on the data, this atom's position is best described statistically
by normal distribution with this (x,y,z) and this temperature factor".
Occupancy is normally 1.0, and when it is not, it means "this atom
occupies two (or more) distinct positions and here are the normal
distribution parameters for one of them". Now substitute zero
occupancy. It says "here are some parameters for an atomic position,
but my atom is not there". What is really happening with weak density
is that you don't know where the atom is (and neither you know where it
is not). So placing any ATOM record is misleading.

It's all semantics, of course.

--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /

CCP4bb navigation

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

Previous message:
Subject: Re: generating omit maps
From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2008-12-11

Next message:
Subject: Re: suggestions for UV spectrometer
From: Pius Padayatti ppadayatti {- at -} GMAIL {- dot -} COM
Date: 2008-12-11