[ccp4bb] Postdoctoral Fellow Position at University of Delaware

Postdoctoral Fellow Position Parashar laboratory at University of Delaware College of Health Sciences, is currently seeking a Postdoctoral Fellow to perform structure-function studies of proteins regulating bacterial signaling.  Qualifications:·  Ph.D. in Biochemistry, Molecular Biology, Stru

Re: [ccp4bb] Looking at an EM map..

EM maps are electron potential maps, fundamentally different from electron density maps in X-ray crystallography. You might also want to check the Protein Science paper by Jimin Wang & Peter Moore, 2017 http://onlinelibrary.wiley.com/doi/10.1002/pro.3060/abstract EM maps are electron potential m

[ccp4bb] Scatter for SAXS

Hello, Anyone knows what the ‘integral of ratio to background’ in the Y-axis of the signal plot represent? -- Best, Rosemary Rosemary Nyamboya Randall Division of Cell and Molecular Biophysics New Hunt's House,3rd Floor, Rm 3.20A Guy's Campus London SE1 1UL Tel: 020-7848-6419 Fax: 020-784

Re: [ccp4bb] Looking at an EM map..

This is discussed, for example, here: http://www.pnas.org/content/114/12/3103 Also, here I calculated the distribution of map values (scaled in r.m.s.) for four groups of atoms: main-chain atoms, side-chain oxygen atoms of ASP and GLU (negatively charged OD1, OD2, OE1, OE2), side chain atoms of AR

Re: [ccp4bb] improper rotation matrix

If you have a copy of MOLEMAN2 lying around, you can use the XYz DIstort command to do exactly this: http://xray.bmc.uu.se/usf/moleman2_man.html#S77 --Gerard On Mon, 12 Mar 2018, Franck Coste wrote: Hi all, I'd like to apply an improper rotation matrix to PDB files but it seems it's not al

[ccp4bb] Software developer to help build public bioimaging archive at EMBL-EBI

Dear all EMBL-EBI is embarking on a project to build a scalable (well into the the 100’s of petabytes and beyond) public archive for bioimaging data which will also become the back-end for EMPIAR (empiar.org ). We are looking for a person with experience in developing softw

Re: [ccp4bb] Looking at an EM map..

I would say so yes, but Garib is the expert on this - I'm only repeating what he told me! Cheers -- Ian On 15 March 2018 at 14:41, Eleanor Dodson wrote: > So if I calculate "structure factors" from a map do I just use the map as > is with the negative values included ? > > Eleanor > > On 15 M

Re: [ccp4bb] Looking at an EM map..

So if I calculate "structure factors" from a map do I just use the map as is with the negative values included ? Eleanor On 15 March 2018 at 14:37, Ian Tickle wrote: > > Hi Eleanor > > Electron scattering factors can be negative for negative ions, > particularly at low d*. For a low-resolution

Re: [ccp4bb] Looking at an EM map..

Hi Eleanor Electron scattering factors can be negative for negative ions, particularly at low d*. For a low-resolution map it means that the electric potential is the opposite sign to what you expected. It's why you often don't see ASP & GLU side-chains in low resolution EM maps. Cheers -- Ian

[ccp4bb] Scientific curator to work with EMDB and EMPIAR data

Dear all EMDB (emdb-empiar.org ) is a public archive for 3D molecular and cellular structures derived from cryo-EM experiments including single-particle and electron tomography. EMPIAR (empiar.org ) started off as a public archive for image data rel

[ccp4bb] Looking at an EM map..

I am pig-ignorant about these ,, but this example has negative values as well as positive.. What does this mean? I thought a well phased map would be pretty well all positive.. Eleanor

[ccp4bb] Call for applications for beamtime at Diamond Light Source

Dear all, The call for applications to use Diamond’s MX and BIOSAXS beamlines from October 2018 – March 2019 is now open for users – these beamlines use the BAG proposal system (http://www.diamond.ac.uk/Users/UserGuide/Prop