[phenixbb] Fluorescence group of eYFP
miyatake at riken.jp
Tue Mar 8 16:13:20 PST 2016
now I found a solution like below;
1) make links using " Extensions > Modeling > Make Link " in Coot
2) Do Ready_Set using the PDB file, and you'll get cif and link.edits files
3) Delete all the lines which contain OXT in the cif file.
4) Involve the cif and link.edits files to the Phenix.refine job
It will work well for the CR2 containing GFP proteins.
On Tue, 08 Mar 2016 15:00:29 -0800
André Hoelz <hoelz at caltech.edu> wrote:
> Have you found a solution that works now? I have noticed the same problem that the OXT atom is incorporated and no bond is formed. I would be grateful if you share your a solution.
> Sent from my BlackBerry 10 smartphone.
> Original Message
> From: miyatake
> Sent: Monday, March 7, 2016 11:07 PM
> To: Pavel Afonine
> Cc: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Fluorescence group of eYFP
> 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
> > >
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