I agree that zero occupancy is a bit ugly, but useful when not sure
whether you will ever see that LYS..
But I dont think it wlll displace bulk solvent - at least not in REFMAC
where an atom with occ=0.0 will not contribute to the atom map. And I
expect this is true for all other structure
Perhaps I was confused by the refinement exclude keyword which
explicitly says that atoms excluded from refinement will contribute to
the mask calculation. Thanks for the correction.
I
would still object to the zero-occupancy atoms on semantic grounds.
Partial occupancy means that an atom
Hi everybody,
I just solved the structures of an enzyme an some variants. In the active site
cavity of each variant I found one or two fragments of PEG1000 bound. I used
PEG1000 in the crystallization condition. Among the enzyme variants the number
of non-hydrogen atoms of these PEG fragments
: [ccp4bb] PEG in the pdb?
To: CCP4BB@JISCMAIL.AC.UK
Date: Thursday, 12 August, 2010, 9:16
Hi everybody,
I just solved the structures of an enzyme an some variants. In the active site
cavity of each variant I found one or two fragments of PEG1000 bound. I used
PEG1000 in the crystallization
PEG solutions contain fragments of all sizes - it is the average size
(however defined by the manufacturer) that is 1000. So technically it
is incorrect to claim that you have PEG1000 molecules bound to your
protein, it is most likely much shorter fragments that can penetrate the
channels in
On Thu, 2010-08-12 at 08:57 +, MARTYN SYMMONS wrote:
Zero occupancy is generally a deprecated way of dealing with missing
density as it is confusing for less experienced user of the
coordinates. I think zero occupancy can be useful during refinement as
the atoms help fill space (or for
, 1954.
44, 1998.
45, 2042.
46, 2086.
47, 2130.
--- On Thu, 12/8/10, Ed Pozharski epozh...@umaryland.edu wrote:
From: Ed Pozharski epozh...@umaryland.edu
Subject: Re: [ccp4bb] PEG in the pdb?
To: CCP4BB@JISCMAIL.AC.UK
Date: Thursday, 12 August, 2010, 17:35
PEG solutions contain fragments
...@umaryland.edu wrote:
From: Ed Pozharski epozh...@umaryland.edu
Subject: Re: [ccp4bb] PEG in the pdb?
To: CCP4BB@JISCMAIL.AC.UK
Date: Thursday, 12 August, 2010, 17:35
PEG solutions contain fragments of
all sizes - it is the average size
(however defined by the manufacturer) that is 1000
