[phenixbb] Constrained groups for occupancy refinment

Pavel Afonine pafonine at lbl.gov
Mon Mar 7 10:58:15 PST 2016


Hi Jan,

great, thanks for letting us know!

Pavel

On 3/7/16 10:56, Jan Abendroth wrote:
> Thanks, Pavel,
> that seems to have fixed it.
>
> Cheers,
> Jan
>
> On Mon, Mar 7, 2016 at 10:17 AM, Pavel Afonine <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> wrote:
>
>     Hi Jan,
>
>     I can only guess without seeing the error message. I think ending
>     "or" in both selection strings are the troublemakers.
>
>     Does this work:
>
>     refinement {
>       refine {
>         occupancies {
>           constrained_group {
>             selection = chain A and resseq 62 and altloc A or \
>                         chain B and resseq 62 and altloc A
>             selection = chain A and resseq 62 and altloc B or \
>                         chain B and resseq 62 and altloc B
>           }
>         }
>       }
>     }
>
>     ?
>
>     Pavel
>
>
>     On 3/7/16 10:02, Jan Abendroth wrote:
>>     Hi all,
>>     I have a case where a residue is in two alternative conformations
>>     for chain A and chain B. This residue (Arg 62) happens to be
>>     close to its NCS mate, such that only conformations A for both
>>     chains or only conformations B can take place at the same time.
>>
>>     I tried to follow guidance from the CNG newsletter 2015/07 and
>>     set up the constrained groups as shown below. However, the
>>     refinement crashes with an AtomSelectionError.
>>
>>     Any ideas what I could have done differently?
>>
>>     Cheers,
>>     Jan
>>
>>     refinement {
>>
>>     refine {
>>
>>      occupancies {
>>
>>      constrained_group {
>>
>>      selection = chain A and resseq 62 and altloc A or \
>>
>>             chain B and resseq 62 and altloc A or
>>
>>      selection = chain A and resseq 62 and altloc B or \
>>
>>             chain B and resseq 62 and altloc B or
>>
>>      }
>>
>>      }
>>
>>      }
>>
>>     }
>>
>>
>>     -- 
>>     Jan Abendroth
>>     Emerald Biostructures
>>     Seattle / Bainbridge Island, WA, USA
>>     home: Jan.Abendroth_at_gmail.com <http://Jan.Abendroth_at_gmail.com>
>>     work: JAbendroth_at_embios.com
>>     http://www.emeraldbiostructures.com
>>
>>
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>
>
>
>
> -- 
> Jan Abendroth
> Emerald Biostructures
> Seattle / Bainbridge Island, WA, USA
> home: Jan.Abendroth_at_gmail.com <http://Jan.Abendroth_at_gmail.com>
> work: JAbendroth_at_embios.com
> http://www.emeraldbiostructures.com

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