Hi Natesh;
I don't know that "density" is necessarily inappropriate: the map gives
potential for each voxel, so potential per volume. I'd think that's a
density.
Unsure about "cryoEM density" though, but this may be a matter of how
the phrase is delineated. I often look at green (and red)
Hi all,
I’m encountering problems installing CCP4 9.0 on a brand-new MacBook Pro (M4
chip, OS 15.1.1). Specifically, when I try to launch the Package Manager
(cntrl-click-open, ccp4sm-uni), the icon does that brief “zoom out” thing, but
then nothing else happens.
I’ve worked my way down from
Hi Gloria
I didn’t see this mentioned (perhaps I missed it). But if you are struggling to
get your initial docking solution, do check that your hand is correct. If
your map is good enough you can possibly get it by building small trial
sections (alpha helices can be good), for more challengin
Dear Gloria,
Already the wonderful chimera, phenix and ccpEM and other
excellent softwares have been highlighted for your requirements.
Along with that, I would like to suggest a small correction. It is not
correct to say 'cryoEM density' or 'cryoEM density map'. X-ray
Crystallog
Thanks Martyn!
I should add that support for our docking software in CCP-EM is fairly new, but
it’s developing quickly. You can run emplace_local there too, though you have
to provide it with the coordinates for the search center — more graphical setup
akin to the ChimeraX interface should come
**
*Dear all,*
*
We’re excited to announce the release of PDBe’s new Ligand Pages, a
significant upgrade to the PDBeChem service! This revamped platform
introduces many new features and offers a more comprehensive and
user-friendly way to explore small molecule data in the Protein Data
Bank
Hi Gloria,
I agree that ChimeraX is the easiest starting point for this. After that, the
CCP-EM suite has a variety of rigid and flexible fitting methods that you can
try (including em_placement in the latest). Also many validation functions,
which are kind of important 😊 Our annual Icknield
Hi Gloria,
Guillaume already mentioned emplace_local, so I’ll just mention that if you get
a recent nightly build of Phenix and the latest version of ChimeraX (plus the
Phenix UI plugin from the toolshed), you can tell it your map has symmetry,
place a monomer, and then it will detect the symme
