[phenixbb] Tracing and refining b-strands at 3.3A resolution

[Phil Jeffrey]

Ralf et al.

My question with this approach is that is there any potential to have a 
negative effect on refining the structure, given that one is introducing 
a number of bonds with relatively high average deviations from the mean 
?  The rest of the bonded (covalent) geometry has an rms in the range 
0.004 - 0.015 (-ish) but this is one to two orders of magnitude tighter 
than a hydrogen bond.  Is the target function sophisticated enough to 
handle this or is there a problem with treating hbonds and covalent 
bonds as peers ?

Phil Jeffrey
Princeton

Ralf W. Grosse-Kunstleve wrote:
> Hi Gino,
> 
>> So my question is, is there a way in Phenix to use a 'reference model'
>> during refinement to force a given stretch of polypeptide chain to
>> 'stay' b-stranded during refinement?
> 
> Nope. But you could use the custom bond definitions to restrain hydrogen
> bonds. The syntax is explained in the phenix.refine documentation;
> an example is below.
> The main trouble is that we don't have an automatic tool to generate
> the bond restraints for you. Maybe others have suggestions how to
> use external programs?
> 
> Ralf
> 
> 
> refinement.geometry_restraints.edits {
>   bond {
>     action = *add delete change
>     atom_selection_1 = "chain G and resname ASP and resid 20 and name N"
>     atom_selection_2 = "chain G and resname GLY and resid 33 and name O"
>     symmetry_operation = None
>     distance_ideal = 2.8
>     sigma = 0.1
>     slack = 0.3
>   }
>   bond {
>     action = *add delete change
>     atom_selection_1 = "chain G and resname GLY and resid 33 and name N"
>     atom_selection_2 = "chain G and resname SER and resid 21 and name O"
>     symmetry_operation = None
>     distance_ideal = 2.8
>     sigma = 0.1
>     slack = 0.4
>   }
> }
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