Dear all,
a bit of a background follow-up to this:
On Tue, Jan 14, 2025 at 09:37:44AM -0500, Yong Tang wrote:
> I do understand PDBe offers electron density maps (8hbk.ccp4 and
> 8hbk_diff.ccp4 separately)- is that our go-to nowadays when we would like
> to inspect the maps of any particular PDB
denvercoder9 - not exactly the same, but similar.
On 14/01/2025 22:09, Gerard Bricogne wrote:
Dear Pavel,
Your comment has been made many times, especially in discussions
that eventually led to the official decision to make room for these
coefficients in the mmCIF dictionary. The idea be
Dear Pavel,
Your comment has been made many times, especially in discussions
that eventually led to the official decision to make room for these
coefficients in the mmCIF dictionary. The idea behind granting them an
independent status and recommending that they should accompany the
deposition
RCSB web site still provides 2fo-fc and fo-fc map coefficients downloads in
mmcif format, calculated from validation package.
And they are also available for download through the wwPDB archive.
Yuhe
On Tue, Jan 14, 2025 at 3:53 PM Pavel Afonine wrote:
> Hi all,
> maps are derived information th
Hi all,
maps are derived information that can be trivially computed using source
data, like reflection data and the atomic model, so there isn’t much point
in keeping them around and maintaining an accession service (which costs
something). If that disappeared, I’d totally understand the reasons!
Y
Dear all,
Thanks to quite a few community members who responded, these are the tips:
1) PDB staff has graciously replied with some essential news that I've
missed (see below); 2) mtz files (and more) could be downloaded from
https://pdb-redo.eu/; 3) In coot, instead of using the "Fetch PDB and Map
Hello, you can download the structure factors as a ...sf.ent file which looks
like mmCIF so probably gemmi can make an mtz or a map for you from that.
Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com
Sent from Proton Mail Android
Original Message
On 14/01/2025 14:37, Yong
may not be able to display the map from cif directly
in Coot but converting to mtz first works.
Yong
From: CCP4 bulletin board On Behalf Of Yong Tang
Sent: Tuesday, January 14, 2025 9:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb] access to the electron density maps of a PDB entry
Dear all,
Taking a random PDB entry 8hbk as an example, at one point of time, we have
access to a phase file called 8hbk_phases.mtz under the download section in
https://www.rcsb.org/structure/8hbk However that option doesn't seem to be
available anymore in general.
I do understand PDBe offers
