[phenixbb] Additional conformations and partially occupied waters
Oleg Sobolev
osobolev at lbl.gov
Fri Jan 15 12:26:51 PST 2016
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> 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>
> 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> 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)
>>
>>
>> 1.
>>
>> 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>:
>>
>>> 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> 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
>>>>
>>>>
>>>>
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>>>
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>>
>>
>>
>> --
>> Folmer Fredslund
>>
>>
>>
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>
>
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