atthew.
>>
>> Sent from Outlook for iOS
>> From: CCP4 bulletin board on behalf of Gloria
>> Borgstahl
>> Sent: Tuesday, November 26, 2024 11:50:18 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] cryoEM molecular replacement This Message Is Fro
Hello Johan and Natesh,
There is more info about the terminology in this article:
https://doi.org/10.1038/s41586-024-07215-4
In brief, yes, "Coulomb potential map" or "electrostatic potential map" is most
correct (as far as I remember). But "cryoEM map" is widely accepted as a
shortcut, and is
_
From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>>
on behalf of Gloria Borgstahl
mailto:gborgst...@gmail.com>>
Sent: Tuesday, November 26, 2024 11:50:18 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] cryoEM
rd <mailto:CCP4BB@JISCMAIL.AC.UK>
On Behalf Of Randy John Read
Sent: 27 November 2024 08:40
To: ccp4bb <mailto:ccp4bb@jiscmail.ac.uk>
Subject: Re: [ccp4bb] cryoEM molecular replacement
Hi Gloria,
Guillaume already mentioned emplace_local, so I’ll just mention that if you get
a recent
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)
ubject: [ccp4bb] cryoEM molecular replacement
Hello Friends, We are finally using cryoEM when the crystallography got too
hard! We have a crystal structure for the hexamer. What is the easiest
software tool to swing a monomer or hexamer into the cryoEM density? Thank you,
Gloria To unsub
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
p
>
> HTH
> m
>
> -Original Message-
> From: CCP4 bulletin board On Behalf Of Randy John Read
> Sent: 27 November 2024 08:40
> To: ccp4bb
> Subject: Re: [ccp4bb] cryoEM molecular replacement
>
> Hi Gloria,
>
> Guillaume already mentioned emplace_local, so
Icknield workshop covers these
techniques, look e.g. at
https://www.ccpem.ac.uk/training/icknield_2023/icknield_2023.php
HTH
m
-Original Message-
From: CCP4 bulletin board On Behalf Of Randy John Read
Sent: 27 November 2024 08:40
To: ccp4bb
Subject: Re: [ccp4bb] cryoEM molecular replacement
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
n behalf of Filip Van
Petegem
Sent: Wednesday, November 27, 2024 2:19:41 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] cryoEM molecular replacement
ChimeraX for a quick visual fit:
https://www.cgl.ucsf.edu/chimerax/
On Tue, 26 Nov 2024 at 15:50, Gloria Borgstahl
mailto:gborgst...@gmail.com&
ChimeraX for a quick visual fit:
https://www.cgl.ucsf.edu/chimerax/
On Tue, 26 Nov 2024 at 15:50, Gloria Borgstahl wrote:
> Hello Friends,
> We are finally using cryoEM when the crystallography got too hard! We
> have a crystal structure for the hexamer. What is the easiest software
> tool to
Hello Friends,
We are finally using cryoEM when the crystallography got too hard! We have
a crystal structure for the hexamer. What is the easiest software tool to
swing a monomer or hexamer into the cryoEM density?
Thank you, Gloria
##
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