A few figures in BMC re truncation effects:

 

http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART1.htm

http://www.ruppweb.org/Garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART2.htm

http://www.ruppweb.org/Garland/gallery/Ch10/pages/Biomolecular_Crystallography_Fig_10-10.htm

 

Best, BR

 

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of 
00000c2488af9525-dmarc-requ...@jiscmail.ac.uk
Sent: Thursday, March 5, 2020 12:21
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A question of density

 

Hello, not sure if anyone has mentioned series termination errors in the 
vicinity of electron dense atoms. The attached is from Glusker & Trueblood and 
might be of interest.

Jon Cooper

 

On 5 Mar 2020 19:00, Jessica Besaw <jbesaw1...@gmail.com 
<mailto:jbesaw1...@gmail.com> > wrote:

Hello Matthias,

 

Excellent point. Most of the the ordered water are easily visible at 2 rmsd. 
The central disordered (or partially occupied) water becomes visible only at 
1.3 - 1.4 rmsd, and it is very visible at 1 rmsd (which I have displayed all of 
the maps). In your opinion, do you think this would be noise? 

 

Jessica

 

On Wed, 4 Mar 2020 at 12:45, Barone, Matthias <bar...@fmp-berlin.de 
<mailto:bar...@fmp-berlin.de> > wrote:

hey Jessica

a tip that might come up later on anyway: once you put every reasonable bit 
into the desity, what I like to to when facing such blobbs: I take a well 
defined water out to create a diff density at a position where I know it is 
real. Having a feeling of how much you have to contour the diff density at that 
point can give you a good feeling how much of noise is actually in your density 
right in between the waters..?

best, matthias

 

Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284

  _____  

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
> on behalf of Jessica Besaw <jbesaw1...@gmail.com 
<mailto:jbesaw1...@gmail.com> >
Sent: Wednesday, March 4, 2020 6:42:34 PM
To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
Subject: Re: [ccp4bb] A question of density 

 

Hey Nukri, 

 

Here are the details: Rwork/Rfree = 0.21 / 0.23 for a 2 Angstrom structure

 

I absolutely agree with you on the refinement. I did previously do that, and I 
attached the picture. 

 

What is the BB?

 

Cheers!

 

Jessica 

 

 

 

 

 

 

On Wed, 4 Mar 2020 at 12:20, Nukri Sanishvili <sannu...@gmail.com 
<mailto:sannu...@gmail.com> > wrote:

Hi Jessica,

You do not say how well is the rest of the structure refined. 

First, you should refine the structure best you can, without placing anything 
in the unclear blob of your interest so to obtain the best possible phases and 
hopefully improve the blob density as well.

Then you should let the BB see what that density looks like. Looking at only 
the list of possibilities has very little value without seeing the density 
itself.

Best wishes,

Nukri

 

On Wed, Mar 4, 2020 at 11:10 AM Jessica Besaw <jbesaw1...@gmail.com 
<mailto:jbesaw1...@gmail.com> > wrote:

Hello friends,  

 

I have a "blob" of density in an active site of my protein. 

 

I am struggling to determine if I should place a water in this spot, if I 
should model it as a disordered water, if the density may be a ligand that I 
have not considered, or if it should be left as unaccounted for density. I 
would like to publish this structure without compromising the science.

 

I have attached several possibilities that I have considered below. 

 

Any suggestions would be appreciated.

 

Cheers!

 

Jessica Besaw

 

 

 

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