[phenixbb] Additional conformations and partially occupied waters

Pavel Afonine pafonine at lbl.gov
Sat Jan 30 18:39:59 PST 2016


Hi All,

FWIW, this scenario is described in

"13 typical occupancy refinement scenarios and available options in 
phenix.refine" article here

http://phenix-online.org/newsletter/

Pavel

On 1/15/16 12:30, Helena Taberman wrote:
>
> Thank you for your help indeed! Renaming them would have never crossed 
> my mind!
>
> Best regards,
>
> Helena
>
> On 15.1.2016, at 22.27, Oleg Sobolev <osobolev at lbl.gov 
> <mailto:osobolev at lbl.gov>> wrote:
>
>> Hi Helena,
>>
>> I just spotted that residue 249 is close to 252. To resolve this, you 
>> will have to rename conformations of residue 249 (exchange A and B 
>> altlocs), assing all partial occupancies to 0.5 to make things simple 
>> and add it to selections:
>>
>> selection = chain A and (resseq 252 or resseq 249) and altloc A
>> selection = chain A and (resseq 252 or resseq 249) and altloc B or 
>> chain S and resseq 1702 and altloc B
>>
>> Renaming is necessary because conformaion B of residue 249 is close 
>> to conformation B of residue 252.
>>
>> Best regards,
>> Oleg Sobolev.
>>
>> On Fri, Jan 15, 2016 at 12:13 PM, Oleg Sobolev <osobolev at lbl.gov 
>> <mailto:osobolev at lbl.gov>> wrote:
>>
>>     Hi Helena,
>>
>>     The problem was in altlocs, occupancies and selections.
>>
>>     First, simple case of 249 residue. I don't see why residue 249 is
>>     relevant to 252 or to water 1702 because it is rather far from
>>     them. Therefore it should be treated separately. Residue 249
>>     simply has 2 alternative conformations of side chain (including
>>     CA atom). We set occupancy of A and B conformations to 0.5 (that
>>     is in your file). Also we need to set occupancy to 1 for N, C and
>>     O atoms in this residue to prevent their occupancy from
>>     refinement (in your file they are also present with 0.5 occupancy).
>>
>>     The second case: coupled conformations of 252 and water 1702.
>>     For partially occupied water molecules you also need to define
>>     appropriate altloc. In your case it is present only when the
>>     residue 252 in B conformation, therefore water molecule also
>>     should have B altloc and partial occupancy (the same as B
>>     conformation of residue 252, 0.49). The residue 252 is split to
>>     alternative conformations completely, and this is OK. Next, to
>>     let phenix.refine know that these conformations are coupled, you
>>     need the following parameter file:
>>     refinement {
>>       refine {
>>         occupancies {
>>           constrained_group {
>>             selection = chain A and resseq 252 and altloc A
>>             selection = chain A and resseq 252 and altloc B or \
>>               chain S and resseq 1702 and altloc B
>>        }
>>       }
>>      }
>>     }
>>     or enter these selections in appropriate place in GUI (in one
>>     constraint occupancy group).
>>
>>     Here each selection will get the same occupancy for all atoms in
>>     it, therefore we have both 252 residue and water residue and use
>>     altloc B. We don't have water with altloc A (but you may consider
>>     it) therefore the first selection contains only residue 252.
>>     These two selections present in one constrained group ensures
>>     that occupancies of these selections will add up to 1.
>>
>>     You can do all the model manipulations in Coot.
>>
>>
>>     I'll send you corrected pdb file shortly off-list.
>>
>>     The useful reading on topic would be
>>
>>     "13 typical occupancy refinement scenarios and available options
>>     in phenix.refine" by Pavel Afonine in the latest Computational
>>     Crystallography Newsletter:
>>
>>     http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12
>>
>>     Case #7 is almost your case, the only difference is one of your
>>     residues is water and it has only one conformation.
>>
>>     Best regards,
>>     Oleg Sobolev.
>>
>>     On Wed, Jan 13, 2016 at 11:59 PM, Helena Taberman
>>     <helena.taberman at uef.fi <mailto:helena.taberman at uef.fi>> wrote:
>>
>>
>>         Hi,
>>
>>         Thanks for your advice. It’s still not working. I use the
>>         phenix gui version and if I set, for example,
>>
>>         chain A and resid 249
>>         chain A and resid 252
>>         chain S and resid 1702
>>
>>         as a constrained group at the occupancy refinement selections
>>         (the two residues have 2 conformations both and the water is
>>         there just if the conformation of residue 252 is B) the
>>         refinement just makes the residues a constrained group alone
>>         making even their main chain occ. something like 0.49 as for
>>         the both of the side chains too. And it also kicks them a bit
>>         out of their densities. So how to continue? What am I doing
>>         wrong?
>>
>>         Best regards,
>>         Helena
>>
>>>         Folmer Fredslund <folmerf at gmail.com
>>>         <mailto:folmerf at gmail.com>> kirjoitti 11.1.2016 kello 15.20:
>>>
>>>         Hi Helena,
>>>
>>>         I believer this is the relevant bit from the manual:
>>>         https://www.phenix-online.org/documentation/reference/refinement.html#occupancy-refinement
>>>         (in the examples)
>>>
>>>         4.
>>>
>>>             Complex occupancy refinement strategy (combination of
>>>             various available occupancy refinement types):
>>>
>>>             % phenix.refine data.hkl model.pdb strategy=occupancies occ.params
>>>
>>>         The amount of atom selections makes it inconvenient to type
>>>         them all from the command line. This is why the parameter
>>>         file occ.params is used and it contains following lines:
>>>
>>>         refinement {
>>>            refine {
>>>              occupancies {
>>>                individual = element BR or water
>>>                individual = element Zn
>>>                constrained_group {
>>>                  selection = chain A and resseq 1
>>>                }
>>>                constrained_group {
>>>                  selection = chain A and resseq 2
>>>                  selection = chain A and resseq 3
>>>                }
>>>                constrained_group {
>>>                  selection = chain X and resname MAN
>>>                  selection = chain X and resseq 42
>>>                  selection = chain X and resseq 121
>>>                }
>>>                remove_selection = chain B and resseq 1 and name O
>>>                remove_selection = chain B and resseq 3 and name O
>>>              }
>>>            }
>>>         }
>>>
>>>
>>>         Hope this helps,
>>>         Folmer
>>>
>>>         2016-01-11 13:14 GMT+01:00 Christian Roth
>>>         <christianroth034 at gmail.com
>>>         <mailto:christianroth034 at gmail.com>>:
>>>
>>>             Hi Helena,
>>>             Indeed you have to group the relevant aa and the
>>>             respective water together in a constrained group to
>>>             avoid your problem and get the occupancies add up to 1.
>>>             This us described in the manual under occupancy
>>>             refinement. I can't access the manual at the moment to
>>>             give you a more detailed answer.
>>>
>>>             Cheers
>>>
>>>             Christian
>>>
>>>             On 11 Jan 2016 11:56, "Helena Taberman"
>>>             <helena.taberman at uef.fi <mailto:helena.taberman at uef.fi>>
>>>             wrote:
>>>
>>>                 Hi,
>>>
>>>                 I’m trying to refine a structure determined to 1.6 Å
>>>                 resolution. There’s several residues with additional
>>>                 conformations and waters with partial occupancies
>>>                 stating that they would be there when the
>>>                 conformation of the residues allows it. When I try
>>>                 to refine these conformations and partially occupied
>>>                 waters together the refinement kicks the second
>>>                 conformations and water molecules out of their
>>>                 densities, since they are obviously too close to the
>>>                 other additional conformations of the residues or
>>>                 the following residues. What could I do? Should I
>>>                 somehow group them together or what?
>>>
>>>                 Best regards,
>>>                 Helena
>>>
>>>                 Helena Taberman, Ph.D.
>>>
>>>                 University of Eastern Finland
>>>                 Department of Chemistry
>>>                 Joensuu Campus
>>>                 P.O. Box 111
>>>                 FI-80101 Joensuu, FINLAND
>>>
>>>                 Mobile: +358 50 337 2488 <tel:%2B358%2050%20337%202488>
>>>
>>>
>>>
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>>>
>>>
>>>
>>>         -- 
>>>         Folmer Fredslund
>>
>>
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