Dear CCP4BB,
I am working on a structure refinement and came across a blob of density
that looks like an anvil (see link). Has anyone seen this before and have
an idea of what it is?
https://drive.google.com/file/d/1BGNwV3MujYjrV4W5m1bh3_WWd49RhJ1w/view?usp=sharing
The protein is in potassium p
Try fitting a xylitol molecule in it but watch out for the distortions
caused by proximity to symmetry axis.
Artem
On Thu, Mar 31, 2011 at 1:16 PM, Shu XU wrote:
> Hi, there.
> I'm refining a 1.76 A structure. The r-work stuck at 21%, rfree is 24%
> after adding waters.
> But there is something
>
> *Vaheh Oganesyan*
>
> *www.medimmune.com <http://www.medimmune.com>*
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
> *Vijaykumar
> Pillalamarri
> *Sent:* Thursday, October 26, 2017 10:24 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:
Hi Vijay,
Why there is no 2mFo-DFc (blue) feature on this mFo-DFc (green) map?!! Is
the contour level for blue map set high?!! If there is no 2mFo-DFc density,
should this be consider as noise?!!
Hope this helps,
Best Wishes,
Partha
On Thu, Oct 26, 2017 at 10:23 AM, Vijaykumar Pillalamarri <
vi
w.medimmune.com/>
>
>
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
> <mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Vijaykumar Pillalamarri
> Sent: Thursday, October 26, 2017 10:24 AM
> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
> Subjec
an, Vaheh > <mailto:oganesy...@medimmune.com>> wrote:
>> Water molecules completing Co coordination?
>>
>>
>>
>> Regards,
>>
>>
>>
>> Vaheh Oganesyan
>>
>> www.medimmune.com <http://www.medimmune.com/>
o.fr
> URLs: http://lcrbw.pharmacie.univ-paris5.fr/ ,
> http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
> ------
>
>
>
> --
> *De :* Nick Pearce
> *À :* CCP4BB@JISCMAIL.AC.UK
> *Envoyé le :* Jeudi 26 octobre
cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ ,
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
De : Vijaykumar Pillalamarri
À : CCP4BB@JISCMAIL.AC.UK
Envoyé le : Vendredi 27 octobre 2017 8h59
ar Pillalamarri
À : Philippe BENAS
Cc : "CCP4BB@JISCMAIL.AC.UK"
Envoyé le : Vendredi 27 octobre 2017 14h08
Objet : Re: [ccp4bb] Unknown electron density
Dear Philippe,
Here is the images showing anomalous map at Co contoured at 5.
Thanks,Vijaykumar
On 27 October 2017 at 14:05,
ippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ ,
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18
De : Vijaykumar Pillalamarri
À : Philippe BENAS
Cc : "CCP4BB@JISCMAIL.AC.UK"
Envoyé le : Vendredi 27 octobre 2017 14h08
Objet : Re: [ccp4bb] Unknown electro
IL.AC.UK"
Envoyé le : Vendredi 27 octobre 2017 14h08
Objet : Re: [ccp4bb] Unknown electron density
Dear Philippe,
Here is the images showing anomalous map at Co contoured at 5.
Thanks,Vijaykumar
On 27 October 2017 at 14:05, Philippe BENAS wrote:
Hello Vijaykumar,
Well, 27 e- * 0.4 =
:58 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unknown electron density
Dear CCP4BB,
I am working on a structure refinement and came across a blob of density that
looks like an anvil (see link). Has anyone seen this before and have an idea of
what it is?
https://drive.google.com/file/d
: [ccp4bb] Unknown electron density
Dear CCP4BB,
I am working on a structure refinement and came across a blob of density that
looks like an anvil (see link). Has anyone seen this before and have an idea of
what it is?
https://drive.google.com/file/d/1BGNwV3MujYjrV4W5m1bh3_WWd49RhJ1w/view?usp=sharing
urent Fries
67404 ILLKIRCH - FRANCE
tel: +33 (0)3 69 48 52 82
From: CCP4 bulletin board on behalf of Betty Chu
Sent: 19 April 2023 18:58:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unknown electron density
Dear CCP4BB,
I am working on a structure refinement and
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Uma Gabale [0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk]
Sent: Tuesday, January 24, 2017 7:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unknown electron density blob
Dear all,
While refining a structure at 2.5 A
On 24/01/2017 17:19, Uma Gabale wrote:
While refining a structure at 2.5 A resolution, we observed a
semi-circular/crescent shaped
electron density blob as shown in the attached picture. We have been unable to
identify it
so far, and would appreciate any help in identification.
If you have C
On 24/01/2017 17:32, Paul Emsley wrote:
On 24/01/2017 17:19, Uma Gabale wrote:
While refining a structure at 2.5 A resolution, we observed a
semi-circular/crescent shaped
electron density blob as shown in the attached picture. We have been unable to
identify it
so far, and would appreciate an
Hi Uma,
It is risky to guess based on one-view of of the density from 2-dimensional
images. What is the contour-level of 2mFo-DFc (blue) map displayed here?!!
If 2mFo-DFc density is continuous from Arg, say at 0.8 sigma, then could it
be an alternate conformation of the Arg side-chain. One could b
PEG. It wraps around K or R residues just like you are showing.
Artem
www.harkerbio.com
"where every blob has candy inside"
On Jan 24, 2017 12:19 PM, "Uma Gabale" <
0ebb5dcf3eaa-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear all,
> While refining a structure at 2.5 A resolution, we observed a
>
Exeter
Ex4 4QD
Tel: + 44 (0)1392 726121
Email: m.viv...@exeter.ac.uk
"I don't want to believe. I want to know". [C. Sagan]
From: CCP4 bulletin board on behalf of Paul Emsley
Sent: 24 January 2017 17:32:35
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [
Just to add to this, in our group, we had a funny case where we found PEG
around K:
https://drive.google.com/open?id=0B2DrnhrLgvwGSldLVl9pSEptakE
https://drive.google.com/open?id=0B2DrnhrLgvwGZlNiYTFoaktPUHc
Ana Luisa
> On 24 Jan 2017, at 17:36, Artem Evdokimov wrote:
>
> PEG. It wraps aroun
:11 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unknown electron density blob
Just to add to this, in our group, we had a funny case where we found PEG
around K:
https://drive.google.com/open?id=0B2DrnhrLgvwGSldLVl9pSEptakE
https://drive.google.com/open?id=0B2DrnhrLgvwGZlNiYTFoaktPUHc
to:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: Re: [ccp4bb] Unknown electron density blob
Some general remarks about PEG modelling and associated caveats:
http://journals.iucr.org/d/issues/2016/12/00/rr5136/index.html
Section 3.6.5.
Best, BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
Dear all,Thank you very much for your replies. It is a PEG, a "di"ethylene
glycol to be precise, in most chains. Best regards,Uma. --Uma Gabale,
PhDResearch AssociateMolecular and Cellular Biochemistry
Indiana University Bloomington
#yiv6125321912 #yiv6125321912 -- _filtered #yiv6125321912
{fo
Uma's use of quotes around "di" suggests a related question about PDB
convention. It was my (perhaps not very good) understanding that ligands should be
identified by what is actually present in the crystal, and not by what can be modeled.
For example endogenous ubiquinone is likely to be UQ50
I've often wondered about PEG (and, I guess, other synthetic polymers):
wouldn't it just be better to define the monomer, and then model a chain of
however many monomers you need?
T
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
Croll<mailto:ti...@cam.ac.uk>
Verzonden: woensdag 25 januari 2017 18:30
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: Re: [ccp4bb] Unknown electron density blob, pdb convention for
partially ordered ligands
I've often wondered about PEG (and, I guess
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