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
ccp4bb] Unknown electron density blob
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, an
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
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
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