[ccp4bb] reliable/unreliable maps?

2012-01-10 Thread Luca Pellegrini
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

Re: [ccp4bb] reliable/unreliable maps?

2012-01-10 Thread Paul Emsley
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?

2012-01-10 Thread Boaz Shaanan
: 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

Re: [ccp4bb] reliable/unreliable maps?

2012-01-10 Thread Gerard DVD Kleywegt
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

Re: [ccp4bb] reliable/unreliable maps?

2012-01-10 Thread Luca Pellegrini
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

Re: [ccp4bb] reliable/unreliable maps?

2012-01-10 Thread Frank von Delft
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

Re: [ccp4bb] reliable/unreliable maps?

2012-01-10 Thread Pavel Afonine
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

Re: [ccp4bb] reliable/unreliable maps?

2012-01-10 Thread Robbie Joosten
- 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

Re: [ccp4bb] reliable/unreliable maps?

2012-01-10 Thread Ed Pozharski
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

Re: [ccp4bb] reliable/unreliable maps? (Deposition of map coefficients)

2012-01-10 Thread Oliver Smart
[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

Re: [ccp4bb] reliable/unreliable maps? (Deposition of map coefficients)

2012-01-10 Thread Pavel Afonine
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