Dear Neno,
when I asked the same question a few months ago, I ended up writing my
own program. We used it for our study of coking in the zeolite ZSM5
(https://doi.org/10.1002/anie.202205413). It is not at all user
friendly, and it reads in FCF files, rather than MTZ files. I can
send you the sourc
Hey Pavel,
Thank you for your thoughtful comments and excellent references.
I also just realized I made a mistake in an earlier message. When you
"integrate" a map using its average value you want to multiply by the
volume of the asymmetric unit, not the volume of the unit cell. If you
mult
Hi James,
- Where exactly inside the blob of density do you place these dummy atoms?
>
> Where? At the peaks.
>
Peaks? This means you need to have atomic resolution data and also blobs
representing ordered atoms, so you actually have peaks!
> What I usually do is pick peaks, put atoms at the hi
Thank you Pavel, responses inline below. There are indeed a lot of
possible approaches, and my experience is far from complete, but I will
share my impressions.
On 8/15/2022 8:15 PM, Pavel Afonine wrote:
Hi James,
I like your approach with dummy atoms and occupancy refinement.
Dealing with
Hi all,
There are lots of great suggestions in this thread. I will just add a
little trick from small molecule crystallography: when trying to estimate
how many atoms can fit in a given volume, you can use the Rule of 18. Take
the volume of interest in Angstroms^3 and divide it by 18 Angstroms^3.
Hi James,
I like your approach with dummy atoms and occupancy refinement. Dealing
with actual maps sounds like hell to me indeed (especially given that we
deal with weighted Fourier maps!). Reading this as someone who immediately
translates this into a computer code (in my mind), a few things that
There are several programs for integrating electron density, but please
let me assure you that it is almost always the wrong thing to do.
A much better strategy is occupancy refinement. Throw in dummy atoms,
turn off non-bonded interactions to them, and refine their occupancy
until it a) stop
Hi Neno
I think you mean the total number of electrons in the volume, i.e. the
volume integral of the electron density, or perhaps you mean the average
electron density, i.e. the total number of electrons in the volume divided
by the volume.
Cheers
-- Ian
On Wed, 10 Aug 2022, 15:00 Neno Vuksa
: Neno Vuksanovic
Date: Wednesday, 10 August 2022 at 16:00
To: "CCP4BB@JISCMAIL.AC.UK"
Subject: [ccp4bb] Quantifying electron density inside of a given volume
Dear All,
I would like to quantify electron density inside of positive Fo-Fc blobs in
active sites of multiple protomers in t
Dear All,
I would like to quantify electron density inside of positive Fo-Fc blobs in
active sites of multiple protomers in the map and compare them. I am aware
that I can interpolate maps and obtain density values at coordinate points
using either MapMan, Chimera or Coot, but I would like to kno
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