[phenixbb] Fluorescence group of eYFP

miyatake miyatake at riken.jp
Tue Mar 8 17:09:28 PST 2016


Dear Nigel,

Thank you for your information.

In my case, the automatic linking did not work well.
I guess my CR2 (fluorescent group) is somewhat distorted.

Even after I delete the OXT atoms in the model, they appeared again
after refinement.


Thus I deleted all OXT lines in the cif file, and then added the cif and link.edits
to the refinement, Now it works.

   Best,

    Miyatake


On Tue, 8 Mar 2016 10:41:47 -0800
Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> Miyatake
> 
> The OXT atom in the restraints file is there because it can be in the
> model. You need to remove the atom from the model if you don't want it.
> 
> Also, Coot's make link does not make a link in Phenix. You need to rely on
> the automatic linking or provide your own. You can check that the link is
> present in the refinement by checking the .geo file.
> 
> Cheers
> 
> Nigel
> 
> ---
> Nigel W. Moriarty
> Building 33R0349, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
> 
> On Mon, Mar 7, 2016 at 11:06 PM, miyatake <miyatake at riken.jp> wrote:
> 
> > 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.
> >
> >     Miyatake
> >
> >
> >
> > 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
> > > >
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