[phenixbb] Help with custom bond restraints syntax

Andy Torelli att29 at cornell.edu
Tue Sep 29 11:05:18 PDT 2009


Thanks Pavel, that works well.

Best,
-Andy

On 9/29/2009 12:21 PM, Pavel Afonine wrote:
> Alternatively, you can do simply this:
> 
> refinement.geometry_restraints.edits {
>    bond {
>         action = *add
>         atom_selection_1 = chain F and resid 1 and name FE1
>         atom_selection_2 = chain A and resid 69 and name SG
>         distance_ideal = 2.35
>         sigma = 0.1
>         slack = None
>    }
> }
> 
> 
> Pavel.
> 
> 
> On 9/29/09 8:54 AM, Andrew T. Torelli wrote:
>> Hi all,
>>
>>      I'm having what I believe is a simple problem defining custom bond
>> restraints between a side chain in my protein model and a ligand
>> (non-covalent bond).  Here is a minimal form of my custom bond
>> definition file that suffers from the error:
>>
>> refinement.geometry_restraints.edits {
>>    Atom1  = chain F and resid 1 and name FE1
>>    Atom2  = chain A and resid 69 and name SG
>>    bond {
>>         action = *add
>>         atom_selection_1 = Atom1
>>         atom_selection_2 = Atom2
>>         distance_ideal = 2.35
>>         sigma = 0.1
>>         slack = None
>>    }
>> }
>>
>>      I'm using phenix 1.4-153 and I get the following error:
>> ERROR: Unused parameter definitions:
>>   refinement.geometry_restraints.edits.Atom1 (file
>> "/HOME/andrew/PHENIX_paramfiles/test.edits", line 5)
>>   refinement.geometry_restraints.edits.Atom2 (file
>> "/HOME/andrew/PHENIX_paramfiles/test.edits", line 6)
>>
>>      I've checked through the online manual and I believe my syntax is
>> correct, but I'm not sure why my custom bond restraint is being
>> ignored.
>>
>>      A second question is: once I get the custom bond/angle restraints
>> correctly implemented, is there a better or more convenient place to
>> look and confirm that the restraints have been imposed other than the
>> .geo file phenix.refine outputs?
>>
>> Thank you very much for your help,
>> -Andy
>>
>>
>>
>>
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