Thursday, 2 February 2012

reliable/unreliable maps? (Deposition of map coefficients)

From: Oliver Smart
Date: 10 January 2012 16:39


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



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


----------
From: Pavel Afonine

Yep, phenix.refine also always creates one reflection file that contains map coefficients. In fact, it contains all together:
- original Iobs (or Fobs - whatever the user specified);
- Fobs used in refinement;
- Fmodel (the total model structure factor including all scales, bulk-solvent etc), so one can readily recompute the R-factor;
- freeR flags;
- and map coefficients (mFo-DFc, 2mFo-DFc and 2mFo-DFc with missing Fo filled in with DFc).

The question is whether the PDB retains this information?

Pavel


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