[ccp4bb] How to assess geometry in a model?

Hi Folks I'm looking for a way to score each atom (or residue) in a model based on it's geometry. I know these scores exists because various software packages speak of outliers, even including a sigma value in some cases. So I'm looking for a simple way to get a complete list (not just outliers)

[ccp4bb] phenix.real_space_correlation vs overlapmap

Hi all I'm trying to 'measure' the density in a region of my structure by integrating the electron density there (notwithstanding errors in F000). I understand that both overlapmap and phenix.real_space_correlation compute density surrounding individual atoms for their calculations. Is there any

Re: [ccp4bb] phenix.real_space_correlation vs overlapmap

On Mon, May 2, 2011 at 12:53 PM, Pavel Afonine wrote: > Hi Matt, > > > I'm trying to 'measure' the density in a region of my structure by >> integrating the electron density there (notwithstanding errors in F000). I >> understand that both overlapmap and phenix.real_space_correlation compute >>

Re: [ccp4bb] phenix.real_space_correlation vs overlapmap

ing to make this whole thing suspect anyway. What I really want is an END map. Have you got code somewhere? I wasn't planning on sleeping tonight anyway... > > -James Holton > MAD Scientist > > On May 2, 2011, at 11:44 AM, Matt Warkentin wrote: > > > Hi all >

[ccp4bb] edit mtz cell in header?

Howdy folks I'm having an infuriating problem with an mtz file and sftools. I'm sure this is an easy fix. Here's the situation: phaser gave me an mtz and pdb file with bad cell information. It's I213, but the cell is listed as 168.981 168.981 168.982 i.e. NOT cubic - this creates an error wi

[ccp4bb] looking for collaboration

structure on cooling, rapid cooling may trap the room temperature ensemble, whereas very slow cooling might give a better-ordered 'annealed' structure. Thank you for your consideration, and please don't hesitate to email me directly with questions. Matt Warkentin

[ccp4bb] how to superpose density maps?

Hi all I have a seemingly simple task that I can't seem to figure out how to do: I have a bunch of structures with same space/cell that I want to compare in coot. It is easy to superpose the models, but I would also like to superpose the maps. Is there a simple way to do this? If not, is that

[ccp4bb] Wilson B-factor from truncate

hi all i'm confused about truncate's Wilson plot output. i'm running truncate version 6.1: 28/03/08 in particular: a) the wilson plot displayed in the output file has as the horizontal axis LABEL: 4 sinsq/lamdasq (i.e. 4 s^2) (times 100, forget about that for the moment) b) the TICK MARKS on

[ccp4bb] another truncate question

hi folks i've almost got my B-factors questions sorted out. one thing i still don't understand is this: in truncate's wilson plot, what is plotted on the vertical axis is not ln I_mean, but ln (I_mean/ff_mean) and ff_mean (or Mn_ff, as truncate calls it) is the "average expected value of ff".