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
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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