[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>
>>>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> <mailto:phenixbb at phenix-online.org>
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>> <mailto:phenixbb-leave at phenix-online.org>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> <mailto:phenixbb at phenix-online.org>
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>> <mailto:phenixbb-leave at phenix-online.org>
>>>
>>>
>>>
>>>
>>> --
>>> Folmer Fredslund
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave at phenix-online.org
>> <mailto:phenixbb-leave at phenix-online.org>
>>
>>
>>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20160130/e8678776/attachment-0001.htm>
More information about the phenixbb
mailing list