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:[log in to unmask]] On Behalf Of
>> Frank von Delft
>> Sent: Tuesday, January 10, 2012 16:23
>> To: [log in to unmask]
>> 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: [log in to unmask]
>>> Tel: 0044-1223-760469
>>> Fax: 0044-1223-766002
>>> Sanger building, room 3.59
>
|