Dear all,
A minor point but worth mentioning, I think...
The EDS server does not produce a density map for PDB entries for which it
cannot calculate R-factors within 5 percentage points of the published values.
I understand that the server was set up in the dark ages of crystallographic
On 10/01/12 13:25, Luca Pellegrini wrote:
Dear all,
A minor point but worth mentioning, I think...
The EDS server does not produce a density map for PDB entries for which it
cannot calculate R-factors within 5 percentage points of the published values.
I believe that the maps are not
: Re: [ccp4bb] reliable/unreliable maps?
On 10/01/12 13:25, Luca Pellegrini wrote:
Dear all,
A minor point but worth mentioning, I think...
The EDS server does not produce a density map for PDB entries for which it
cannot calculate R-factors within 5 percentage points of the published values
There can be many different reasons why EDS calculates an R-value that is
different from the one reported by the authors - some of these are listed
here: http://eds.bmc.uu.se/eds/eds_help.html#PROBLEMS
Back in the dark ages (actually, the late 90s) we arbitrarily decided to use
a tolerance of
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
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
Or just print both Rfactors...?
This is what phenix.model_vs_data does, leaving for you to decide if the
difference is significant:
http://phenix-online.org/documentation/model_vs_data.htm
Pavel
-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Frank von Delft
Sent: Tuesday, January 10, 2012 16:23
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] reliable/unreliable maps?
Or just print both Rfactors...?
On 10/01/2012 15:21, Luca Pellegrini wrote:
Hi Paul
On Tue, 2012-01-10 at 13:25 +, Luca Pellegrini wrote:
This is not a reliable map.
There are many reasons why one could get the gap in R-values. As the
proud author of an unreliable map myself (3pht), I found that what did
it was that the TLS-refined model was deposited with the full
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Frank von Delft
Sent: Tuesday, January 10, 2012 16:23
To: CCP4BB@JISCMAIL.AC.UK
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
after I sent a bug report to the PDB (e.g. 3mbs).
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Frank von Delft
Sent: Tuesday, January 10, 2012 16:23
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] reliable/unreliable maps
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