Hi Nick, Robbie,
I encountered the same problem. This is not a bug but the way the data was
deposited.
They have deposited intensities. What I did to be able to look at the maps:
Retrieve the "structure factor" file, which in fact contains intensities
Run it through Truncate to get Fs
Remove the ligand from the PDB
REFMAC still refused to read in the new mtz file, for a reason I could
not find. But BUSTER took it without problem
Then look at the electron density in COOT... if the ligand was properly
present, it should come clearly in the difference density
Magali Mathieu
Head of SB-X2S
Sanofi LGCR - SDI
Centre de Recherche de Vitry/Alfortville TÉL. : +33 (0) 1.58.93.39.90 - FAX :
+33 (0) 1.58.93.80.63 13, quai Jules Guesde – BP 14 – 94403 Vitry-sur-Seine
Cedex France
Please consider the environment before printing this email!
-----Message d'origine-----
De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Robbie
Joosten
Envoyé : vendredi 29 août 2014 15:48
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] KRAS maps
Hi Nick,
Not sure what happened here, it seems like a bug in this EDS entry. You can try
PDB_REDO for maps. In recent versions of COOT (version 0.8*) the button for
getting maps and a model is just under that for EDS. There is a plugin for
older versions of COOT. They look okay, but the model has changed (on purpose).
If you prefer looking at maps for an unmodified model you can download the mtz
files here:
http://www.cmbi.ru.nl/pdb_redo/lu/4luc/4luc_0cyc.mtz.gz
http://www.cmbi.ru.nl/pdb_redo/lv/4lv6/4lv6_0cyc.mtz.gz
Cheers,
Robbie
> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Nicholas Larsen
> Sent: Friday, August 29, 2014 15:36
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] KRAS maps
>
> Dear All,
> I frequently use the Coot feature "Fetch PDB and MAP using EDS..."
> with great success when peer reviewing literature reports. However,
> when I try this for the recent KRAS structures deposited by Kevan
> Shokat and Jim Wells (Nature 2013), the Coot generated maps are garbage,
> although the
> resolution is better than 1.5 A. Does anyone have an explanation? I also
> checked with one kind colleague at another institute and she confirmed
> my problem using Linux platform (I am using Windows).
>
> See PDBs, 4LUC and 4LV6, for example.
>
> Cheers,
> Nick
>
>
>
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