Re: [ccp4bb] quantifying electron density

(14):7727-36. doi: 10.1128/JVI.78.14.7727-7736.2004. PMID: 15220447; PMCID: PMC434083. Cheers Wim De: "Hughes, Jonathan" À: "CCP4BB" Envoyé: Mercredi 28 Juin 2023 18:16:22 Objet: [ccp4bb] quantifying electron density hello everyone, is there software that can use

Re: [ccp4bb] quantifying electron density

Dear Sriram, dear Jon, The sum of values of a map (always calculated at some finite resolution) is not the same as a sum of density values. In such maps, a contribution of each atom is a function oscillating with the distance to the atomic center. Even when the height of these ripples is

Re: [ccp4bb] quantifying electron density

Dear Pavel, I came across an example of calculating "electron_sums_around_atom" in cctbx . If we don't zero the F000 or if we normalize the density of the real-space map by the unit cell

Re: [ccp4bb] quantifying electron density

Hi Jon, not really the answer to your question but.. This may be very tricky to do because what you look at is not an electron density map but its Fourier image of finite resolution phased by crystal model (that has errors), plus experimental errors, and missing F000 (which is not measured as part

[ccp4bb] quantifying electron density

hello everyone, is there software that can use an electron density map to quantify the number of electrons in a selected volume somewhere in a protein? cheers jon -- Professor Jon Hughes, BSc, PhD Department of Physics Free University of Berlin Arnimallee 14 14195 Berlin Germany mobile: 

Re: [ccp4bb] Quantifying electron density inside of a given volume

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

Re: [ccp4bb] Quantifying electron density inside of a given volume

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

Re: [ccp4bb] Quantifying electron density inside of a given volume

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

Re: [ccp4bb] Quantifying electron density inside of a given volume

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

Re: [ccp4bb] Quantifying electron density inside of a given volume

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.

Re: [ccp4bb] Quantifying electron density inside of a given volume

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

Re: [ccp4bb] Quantifying electron density inside of a given volume

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)

Re: [ccp4bb] Quantifying electron density inside of a given volume

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

Re: [ccp4bb] Quantifying electron density inside of a given volume

-To: 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

[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 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