Thank you Pavel for the clarification!
What I was really trying to point out is that a missing atom, occ=0.00
and occ=0.01 are not as similar as one might naiively think. Also, if
you put a ligand into a pocket and the occupancy refines to 0, that
does not necessarily mean the ligand is
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From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von
Delft
Sent: 13 June 2014 10:45
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Invisible atoms in ligands
Hi
Dear James
You seem to be discounting the possibility of a true vacuum inside a
structure, which is obviously not the same thing as 'something' (bulk
solvent or whatever). I accept that this is unlikely in the case of ligand
binding sites exposed to solvent, or indeed any site on the outer
Dear Ian,
This has been discussed in a review and related articles by Brian
Matthews and Liljun Liu:
Matthews BW, Liu L. A review about nothing: are apolar cavities in proteins
really empty? Protein Sci. 2009 Mar;18(3):494-502. doi: 10.1002/pro.61. Review.
PubMed PMID: 19241368; PubMed
Dear Daniel
Thanks for the info. I knew that Brian Matthews' group had done some work
in this area.
Cheers
-- Ian
On 16 June 2014 11:16, Daniel Picot daniel.pi...@ibpc.fr wrote:
Dear Ian,
This has been discussed in a review and related articles by Brian
Matthews and Liljun Liu:
The principle difference between occ=0 and omitting the atom entirely is
that occ=0 atoms exclude bulk solvent. Or at least they do for typical
operation of contemporary refinement programs. So, by defining occ=0
you are forcing all map voxels within ~0.6A or so of your invisible
atom to
Hi James,
a remark: different programs may treat occ=0 differently. In phenix.refine
(phenix.maps, etc) atoms with zero occupancy will be ignored for
bulk-solvent mask calculation, unless you ask to do otherwise. For example,
this means that if you want to calculate a ligand OMIT map both options
Hi all - talking about ligands, a quick question on that old conundrum,
of what to do about invisible atoms -- build them with occ=0, or omit them?
For bits of protein, I know all the arguments; personally I prefer
omitting atoms because:
* for amino acid sidechains, their presence is
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Hi Frank,
if you can calculate their position, i.e. it is part of a rigid group,
I would leave it. If it is flexible, I would remove it because the
reader of my deposited structure may not be a crystallographer and
misinterpret the result.
If it is
Hi Frank,
I agree with what Tim has just posted.
Personally I would not think occupancy=0, since this would mean the atom is
not where you placed it (i.e. nowhere near). This could be useful if all
your ligand has the same partial occupancy or, if you have multiple poses,
the sum of occupancies
and leaves extra
room for errors and misunderstandings.
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Tim Gruene
Sent: Friday, June 13, 2014 12:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Invisible atoms in ligands
-Original Message- From: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent:
Friday, June 13, 2014 12:04 To: CCP4BB@JISCMAIL.AC.UK Subject:
Re: [ccp4bb] Invisible atoms in ligands
Hi Frank,
if you can calculate their position, i.e. it is part of a rigid
group, I
@JISCMAIL.AC.UK] On Behalf Of
Tim Gruene
Sent: Friday, June 13, 2014 12:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Invisible atoms in ligands
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Hi Frank,
if you can calculate their position, i.e. it is part of a rigid group,
I
Joosten; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Invisible atoms in ligands
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Hi Robbie,
maybe it is good not to use coordinates for calculations if you cannot
measure the coordinates?
Cheers,
Tim
On 06/13/2014 12:35 PM, Robbie Joosten
modified.
Cheers, Robbie
-Original Message- From: Tim Gruene
[mailto:t...@shelx.uni-ac.gwdg.de] Sent: Friday, June 13, 2014
13:37 To: Robbie Joosten; CCP4BB@JISCMAIL.AC.UK Subject: Re:
[ccp4bb] Invisible atoms in ligands
Hi Robbie,
maybe it is good not to use coordinates
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