[phenixbb] Additional conformations and partially occupied waters

Oleg Sobolev osobolev at lbl.gov
Thu Jan 14 10:49:21 PST 2016


Hi Helena,

My best guess is that either your selections or altloc in .pdb file are
wrong.

We are glad to help you with this issue! To get the precise answer to your
question we need your model and data files (.pdb and .mtz files, and .cif
files for ligand if any). Please send them to me directly (off-list) and
indicate the residues (atoms) in question.

Your data will be kept in confidence.

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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