t;
>
>
> From: CCP4 bulletin board On Behalf Of S
> Sent: Monday, February 21, 2022 21:34
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Negative density
>
>
>
> Hi All,
>
>
>
> I am getting this negative density in the centre of the ring.
Behalf Of S
Sent: Monday, February 21, 2022 21:34
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Negative density
Hi All,
I am getting this negative density in the centre of the ring. Could you please
help me with this?
Resolution: 1.7A
2FoFc - 1.5
FoFc - 3.0
Thanks in advance
or perhaps something in the non-visible part of the ligand pulling electrons
out of the rings? can this somehow be specified as ligand input?
on the other hand, I guess this is near the "end" of refinement, so the Fo-Fc
difference map is probably very flat - meaning that 3 sigma corresponds to ve
I thought it was tryptophan but the nitrogen and extra bond are in the wrong
places so it must be a ligand and, if so, have you tried refining the
occupancy? Cheers, Jon.C.
Sent from ProtonMail mobile
Original Message
On 22 Feb 2022, 05:34, S wrote:
> Hi All,
>
> I am getting
Hi Eze -
I’m glad to see you solved your problem.
On Jun 2, 2014, at 9:07 PM, Eze Chivi
mailto:ezech...@outlook.com.ar>> wrote:
Thanks to everyone for the useful information.
I refined my structure in the reduced form (using the method suggested by
Pavel). Negative density disappeared, and als
Mon, 2 Jun 2014 09:31:28 -0700
>From: CCP4 bulletin board (on behalf
of Pavel Afonine )
>Subject: Re: [ccp4bb] negative density around disulfide bond
>To: CCP4BB@JISCMAIL.AC.UK
>
> Ezequiel,
> since you mentioned you tried Phenix too:
> in Phenix you can remove a p
Ezequiel,
since you mentioned you tried Phenix too:
in Phenix you can remove a particular disulfide bond by using a parameter,
for example:
disulfide_bond_exclusions_selection_string="(chain A and resseq 1 and name
SG) or (chain B and resseq 10 and name SG)"
This works in the command line and G
I have seen similar features fairly often when the data collection has been
pushed to the limit.
The theory is that it is due to radiation damage - you could check by only
merging say the first 50% of your data, then seeing if the di-sulphide is
intact in those maps. ( wouldnt re-refine much - jus
@JISCMAIL.AC.UK Subject: [ccp4bb] negative
density around disulfide bond
Hello, when I refine my structure, I see negative density around the
disulfide bond. I have 7 copies per ASU, and I can see this density in many of
them. In some cases, I see positive density also (negative in the center of
Hi,
I would guess radiation damage, see Weik et al., 2000, PNAS 97, 623-628 or for
a more recent discussion and thorough overview Sutton et al., 2013, Acta Cryst
D69, 2381-2394.
best regards
Marjolein
On 02 Jun 2014, at 07:08, Eze Chivi
mailto:ezech...@outlook.com.ar>> wrote:
Hello, when I
On Jun 1, 2014, at 10:08 PM, Eze Chivi wrote:
> Hello, when I refine my structure, I see negative density around the
> disulfide bond. I have 7 copies per ASU, and I can see this density in many
> of them. In some cases, I see positive density also (negative in the center
> of the straight lin
What I would do - not net ideal!
1) the ASP looks in the wrong place - shift it into green density and one
OE is probably a water..
2) MET notoriously hard to model - I suspect there often are multiple
conformations.. And of course at some wave lengths the S contribution
should be down weighted by
Alaksa,
1) What rmsd / sigma are you contouring your density at ? i.e. are you down in
the "noise" or are you at a reasonable value for your Fo-Fc map?
2) It looks like some of your side-chains appear to have more than one
conformation - it's fairly easy in Coot to position and model both.
To
I assumed that since this topic came up fairly recently, in fact 3
weeks ago (see thread starting from
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg23628.html), it
wasn't just a re-run of the same question.
Perhaps the original poster could clarify whether we are talking about
unexplained
There may be several reasons.
1) Artefacts (some of them)
a) effect of mask: if there are large holes inside molecule and there
should be no electron density (for example hydrophobic holes) then in older
versions masks would put a constant density there and as a result difference
map would
Sounds like rad dam to me. See Burmeister, W. (2000)."Structural
changes in a cryo-cooled protein crystal owing to radiation damage",
Acta Cryst. D 56, 328-341. The first sign of a Met loosing its S-CH3
group will be a negative difference peak on the S.
-James Holton
MAD Scientist
On 11/2
On Wed, Nov 23, 2011 at 7:57 AM, Ian Tickle wrote:
> On 23 November 2011 07:54, Careina Edgooms wrote:
>> I have a question about a 2F0-Fc difference map that I calculated with
>> Refmac.
>
> On 23 November 2011 15:40, Nat Echols wrote:
>> The negative density around Met S could be radiation da
On 23 November 2011 07:54, Careina Edgooms wrote:
> I have a question about a 2F0-Fc difference map that I calculated with Refmac.
On 23 November 2011 15:40, Nat Echols wrote:
> The negative density around Met S could be radiation damage.
But you wouldn't expect to see -ve density in the 2Fo-Fc
On Tue, Nov 22, 2011 at 11:54 PM, Careina Edgooms
wrote:
> I have a question about a 2F0-Fc difference map that I calculated with
> Refmac. In some instances it gives me negative (red) density around part of
> a side chain and no positive density in sight. Furthermore the entire
> residue fits wel
or alternate confonformers against the
>> density for CA.
>>
>>
>>
>> Alternatively, your side chain B-factor restaints might be too tight.
>>
>>
>>
>> Anthony
>>
>>
>>
>>
>>
>> ____
>> From: CCP4 bulletin board [CCP4BB@JISCM
restaints might be too tight.
Anthony
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Careina Edgooms
[careinaedgo...@yahoo.com]
Sent: Wednesday, 23 November 2011 6:54 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] negative density in difference map
Subject: [ccp4bb] negative density in difference map
Good morning CCP4 members
I have a question about a 2F0-Fc difference map that I calculated with Refmac.
In some instances it gives me negative (red) density around part of a side
chain and no positive density in sight. Furthermore the entire
Good morning CCP4 members
I have a question about a 2F0-Fc difference map that I calculated with Refmac.
In some instances it gives me negative (red) density around part of a side
chain and no positive density in sight. Furthermore the entire residue fits
well into the blue density of the compl
Waight, Andrew schrieb:
Hello everyone I have a question for the experts.
I am in the final stages of refining my model placing waters and whatnot. However when I refine my model against the pure scalepack output, I see some rather signifigant negative difference density
Hi Andrew,
If there is no *protein* model built into this region of the map, then it
will be modelled by the bulk solvent correction - therefore, the negative
peaks are telling you that the mean electron density there is lower than
in the bulk solvent. Probably.
Joe
> Hello everyone I have a ques
Yes, I've seen this behavior. I attribute it to lack of the 0,0,0 and ultra-low
resolution reflections. Remember that the average density in a map (with
difference
coefficients or whatever) is zero. That means that if the model lacks a few
atoms,
but has no atoms that don't belong, so that an ab
Indeed there are radicals, but they are not free.
Perhaps a better terminology for them would be "fixed radicals".
Species such as the disulphide radical have been well established by
spectrophotometric and other evidence (M. Weik et. al. and others). It
is quite remarkable actually how long
ironment. This is more
likely to happen on the outside of the protein rather than in the
interior.
Cheers
Colin
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Ian Tickle
Sent: 06 May 2008 11:26
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Ne
r
of cases).
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Lijun Liu
> Sent: 05 May 2008 21:37
> To: James Holton
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Negative density around C of COO-
>
> I believe so
Narayanan Ramasubbu a écrit :
Dear all:
I am noticing that in some of my structures, at 1.5 A resolution, 1)
there is some negative density around the C of the carboxyl groups.
2) I also notice the negative density around S in a disulfide region.
It is as though the disulfide is broken.
Could
Hi James,
We used to talk about primary and secondary radiation damage. The former
operates at room temperature where free radicals were said to be formed
in solution and diffuse around to damage proteins. Under cryoconditions
this no longer happens, leading to greatly improved crystal life ti
I believe some, may not be all, negative density may be due to the
choice of wavelength. C,O and N are not so sensitive to normally
used wavelength (1-1.54A), but S does. This is more true when you
have higher resolution and better quality data. You can estimate
this by f'.
By the way,
I don't mean to single anyone out, but the assignment of "free radicals"
as the species mediating radiation damage at cryo temperatures is a "pet
peeve" of mine. Free radicals have been shown to mediate damage at room
temperature (and there is a VERY large body of literature on this), but
ther
Narayanan Ramasubbu wrote:
Dear all:
I am noticing that in some of my structures, at 1.5 A resolution, 1)
there is some negative density around the C of the carboxyl groups.
2) I also notice the negative density around S in a disulfide region. It
is as though the disulfide is broken.
Could some
I would suspect radiation damage for the S density . I have not seen
radiation damage of only COO carbons, but then again, I do not routinely
get such good diffraction.
Kevin P Madauss V-161a
US Structural Biology GlaxoSmithKline
Office: 919.483
Dear all:
I am noticing that in some of my structures, at 1.5 A resolution, 1)
there is some negative density around the C of the carboxyl groups.
2) I also notice the negative density around S in a disulfide region. It
is as though the disulfide is broken.
Could some body enlighten me on this
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