[phenixbb] cyclic peptide refinement

wei xia weixia1984 at outlook.com
Thu Dec 12 11:37:38 PST 2013


Hi,

It works well.
I appreciate it!

Wei

> On Dec 12, 2013, at 11:52 AM, "Ryan Spencer" <rspencer at uci.edu> wrote:
> 
> Hi Wei,
>  
>                 I used Custom geometry restraints under the Refinement settings tab in phenix.refine. Select the bond you want to make, the angle and the plane you want to set. Should look something like this for the bond:
>  
> chain 'A' and resid '   1 ' and name ' N  ' and altloc ' '; chain 'A' and resid '  16 ' and name ' C  ' and altloc ' '.
>  
> This will create a bond between the amine at position 1 and the carbonyl at position 16. Enter the appropriate distance (1.329) and sigma (0.06).
>  
> The same can be done for the angle and the plane.
>  
> Ryan
>  
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of wei xia
> Sent: Thursday, December 12, 2013 8:14 AM
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] cyclic peptide refinement
>  
> Hi, 
> I am trying to refine a structure with a cyclic peptide ligand.
> I create a 'TRANS' link between the C-ter and N-ter residues of the cyclic peptide during refinement.
> But there is obvious no bond formed between the two residues in the refined structure.
> I checked the geo file and found that there are only angle restraints but no bond restraints between the two residues
> Anyone can help me out?
> Thanks in advance!
>  
> Wei
>  
>  
> P.S. 
>  
> refinement.pdb_interpretation.apply_cif_link {
>  
>        data_link = TRANS
>  
>        residue_selection_1 = chain D and resname MVA and resid 5005
>  
>        residue_selection_2 = chain D and resname ARG and resid 5001
>  
>      }
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