[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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