Re: [phenixbb] Fluorescence group of eYFP

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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Mon, Mar 7, 2016 at 11:06 PM, miyatake wrote:

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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:

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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:

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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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