Re: [phenixbb] Fluorescence group of eYFP

Hello, 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. Best, Miyatake On Tue, 08 Mar 2016 15:00:29 -0800 André Hoelz 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: [email protected] 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.

Miyatake

On Mon, 7 Mar 2016 08:40:21 -0800 Pavel Afonine 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]