Including the final map coefficients as part of the structure factor file
deposited and then archived by the PDB provides a means to directly
see the actual map as interpreted by the crystallographer. EDS is useful
in providing a "third party view" but the actual map is really better.
We think map deposition is a good idea and are working on tools to make it
easy to do with BUSTER. There are already a few recent (REFMAC)
depositions with map coefficients in the pdb (for instance 3u57).
Displaying the maps is currently a bit difficult, see ccp4bb
message (Wed, 21 Dec 2011):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;325e1870.1112
Cheers,
Oliver
| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK |
| http://www.globalphasing.com/people/osmart/ |
On Tue, 10 Jan 2012, Robbie Joosten wrote:
Hi Frank,
EDS already does that. Even so, reproducing the R-factor does not prove that
the map is reliable. See for instance 3frk for which the deposited dataset
is much smaller and less complete than the one used for refinement. The map
from EDS is therefore completely model biased.
I only recently started looking for this problem of lower-than-reported
completeness with. I have not found a lot of cases, but already too many.
Fortunately, at least a few depositors deposited the rest of the dataset
after I sent a bug report to the PDB (e.g. 3mbs).
Cheers,
Robbie
-----Original Message-----
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of
Frank von Delft
Sent: Tuesday, January 10, 2012 16:23
To: [email protected]
Subject: Re: [ccp4bb] reliable/unreliable maps?
Or just print both Rfactors...?
On 10/01/2012 15:21, Luca Pellegrini wrote:
Hi Paul,
What would you rather it say, I'm happy to change the message. "The EDS
does not think that this is a reliable map, in that it is or may be
inconsistent
with what the authors were looking at during deposition"?
How about "Warning: the R-factor calculated for this map differs
significantly from the published R-factor"?
Then we can discuss what is significant ;-)
Luca
Luca Pellegrini
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
Cambridge CB2 1GA - UK
Email: [email protected]
Tel: 0044-1223-760469
Fax: 0044-1223-766002
Sanger building, room 3.59
