Hi Betty,
I've seen very similar looking similar looking density from trifluoroacetic
acid that was present with a synthetic peptide. Could be something to check if
you have a peptide bound.
Best,
Alastair
~
Alastair McEwen, PhD
Integrated Structural Biology Platform
IGBMC
1 rue Laurent Fr
Hi Betty,
You may use the two following applications from the minor lab :
CheckMyMetal - https://cmm.minorlab.org/
CheckMyBlob - https://cmm.minorlab.org/
Best, Anat.
From: CCP4 bulletin board On Behalf Of Betty Chu
Sent: Wednesday, 19 April 2023 19:59
To: CCP4BB@jiscmail.ac.uk
Subject: [ccp4b
Anomalous data might have been helpful. Zinc has an edge at 1.2837 A.
===
All Things Serve the Beam
===
David J. Schuller
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 =
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
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,
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
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
I agree that the difference density isn’t “noise". However, just because it’s
not noise doesn’t mean that it is modellable (with an atomic model) — the
crystallographic density is an average over billions of molecules, and if its
not obvious at 1.6Å what is bound, then it’s probably a superposit
Hi,
Given the weakness and shapelessness of the density I doubt it is "one
conformation of one thing", but rather a superposition of "one or more
conformations of one or more things”. If that is the case then there probably
isn’t enough information in the electron density or enough prior inform
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
Dear Dr. Vaheh,
I tried fitting waters around Co but the positive density is still present
even after refinement.
Thanks,
Vijaykumar
On 26 October 2017 at 20:19, Oganesyan, Vaheh
wrote:
> Water molecules completing Co coordination?
>
>
>
> *Regards,*
>
>
>
> *Vaheh Oganesyan*
>
> *www.medimmun
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
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
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
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
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
: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
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
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: [
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
>
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
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
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
Hi,
Could it be a segment of peg3350?
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
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
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