[phenixbb] Fluorescence group of eYFP

miyatake miyatake at riken.jp
Mon Mar 7 23:06:50 PST 2016

Dear Pavel,

Thank you for your e-mail.

The bonds I want to connect are  between CR2 and amino acids like below;

C PHE A 64 N1 CR2 A 66
C3 CR2 A 66 N LEU A 68

so I made links by the "make link" of Coot.

Then I made .cif file by the Ready_Set, but I noticed
it always contained OTX terminator atom of CR2, so the CR2 connections
to the next amino acids were something wrong after refinement if I used the cif
as it was.

Thus I deleted OTX in the cif file, and then in turn it went well.

I wonder why the cif file contained OTX, is it something a bug?

Thank you for your attention.


On Mon, 7 Mar 2016 08:40:21 -0800
Pavel Afonine <pafonine at lbl.gov> wrote:

> Hi Miyatake,
> could you please send me (and copy to Nigel) the PDB file (and any 
> ligand CIF files you use) and tell what bonds you are expecting to have 
> and that brake as result of refinement.
> Thanks,
> Pavel
> On 3/7/16 03:40, miyatake wrote:
> > Dear all,
> >
> > I'm trying to a mutant of eYFP, which has fluorescence group,
> > CR2.
> >
> > During the refinement, however, the bonds between the CR2 and other amino acids
> > were cleaved even I added the cif file created by the ReadySet.
> >
> >
> > Would some one give me suggestions to solve the problem?
> >
> >     Miyatake
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> > Unsubscribe: phenixbb-leave at phenix-online.org

More information about the phenixbb mailing list