On 27/08/14 23:11, Santarsiero, Bernard D. wrote:
I appreciate all of the comments and suggestions on how to locate a better
CIF file for ATP. I adopted the suggestion of Boaz, and generated a new
ATP.cif file, and refined one of my structures.
Grade is what I would have recommended, FWIW.
T
.@bgu.ac.il
> > Phone: 972-8-647-2220 Skype: boaz.shaanan
> > Fax: 972-8-647-2992 or 972-8-646-1710
> >
> > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> > Bernard D Santarsiero [b...@uic.edu]
> > Sent: Wednesday, August 27, 2014 6:12 PM
>
.il
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
> Bernard D Santarsiero [b...@uic.edu]
> Sent: Wednesday, August 27, 2014 6:12 PM
> To: CCP4BB@JISCMAIL.AC.UK
-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernard D Santarsiero [b...@uic.edu]
Sent: Wednesday, August 27, 2014 6:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ATP library file in REFMAC
I recently refined a structure
Down load the MOGUL coordinates and use some program - PRODRG LIBCHECK
ELBOW to make a new dictionary.. Then check it!
You can assign that dictionary as LIBIN and the new ATP will have
precedence over the wrong one.
Eleanor
On 27 August 2014 18:25, Matthias Zebisch <
matthias.zebi...@bbz.uni-lei
Cant you edit the ATP.cif on your computer to have the correct expected
bond length?
Best, Matthias
-
Dr. Matthias Zebisch
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive,
Oxford OX3 7BN, UK
Hi Bernie,
This is an issue that the REFMAC developers and the PDB are
aware of (at least at the EBI site) and that we have also encountered in a
recent deposition. The problem is that there is indeed a discrepancy between
the stereochemistry for ATP and ADP as defined in the
I recently refined a structure in CCP4/REFMAC with ATP in the structure. Upon
submission to Acta for publication, the wwPDB validation report was run.
Several things were flagged, including the C4-C5 bond in the adenosine moiety
as being too long. It generally refines to 1.46-1.47A. The "ideal"
