[phenixbb] Question about restrain of a nonstandard peptide

[Pavel Afonine]

Hi Yufan,

I suggest you generate CIF for each individual non-standard item in your 
PDB file first. If you are using recent Phenix it should link them 
together automatically (link_ligands=True is responsible for this, and 
it is the default).

Make sure it linked them all correct. It relies on input model geometry, 
so if geometry is suboptimal it may not link them correctly.

Alternatively, you can use custom bond restraints that allow you to link 
any pair of atoms, any number of pairs:

http://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles

You can compose a file like shown in above link and give it to 
phenix.refine GUI or command line, whatever you use.

LINK records are not recognized and used by phenix.refine.

Let me know if you have any questions or need help!

Pavel


On 6/30/16 08:28, Yufan Wu wrote:
> Dear Phenix Developers/Users,
>
> I have a question regarding how to generate a correct restrain for a 
> whole nonstandard peptide and how do run refinement correctly.
>
> The nonstandard peptide in my structure is pepstatin A (IVA Val Val 
> STA Ala STA).
>
> I manually put the pepstatin A in the density and generated the cif 
> files for IVA and STA and run the refinement with them.
>
> After refinement, the whole pepstatin A explored as pieces, which I 
> guess the program treated the pepstatin A as single amino acids.
>
> By the way, I also manual input the “LINK” information in the input 
> pdb file as below,
>
> LINK         C   VAL L   3                 N   STA L   4     1555   1555
> LINK         N   ALA L   5                 C   STA L   4     1555   1555
> LINK         C   ALA L   5                 N   STA L   6     1555   1555
>
> And also, when I use the “Real Space Refine Zone” by clicking two 
> atoms for the whole pepstatin A in coot, it exploded again, although I 
> input the same cif file in coot as well.
>
> The data quality is not good (2.9 A with CC1/2=12), thus it is 
> difficult to place amino acid individually to fit the destiny.
>
> In the PDB, there are several structures containing the pepstatin A, 
> such as 4TVG, 4AUC. They have the pepatatin A sequence as VVVXAX, but 
> none of them lists the constrains.
>
> Would you please help me and let me know how can I continue with 
> refinement? Please let me know if you need more information.
>
> Thank you vey much!
>
> Yufan Wu
>
>
>
>
> Regards,
>
> Yufan Wu
> The Plueckthun Lab
> www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>
> Phone: +41 44 635 5574
>
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