# [phenixbb] alternative conformations

Pavel Afonine pafonine at lbl.gov
Wed Feb 13 11:11:10 PST 2008

```Hi Colin,

just to add to Ralf's reply...

If you need an example, here is file containing atoms in alternative
conformations that will be automatically recognized by phenix.refine:
http://www.rcsb.org/pdb/files/1a6m.pdb

Currently phenix.refine can do the following types of occupancy refinement:

1) Individual (just refine occupancies of atoms without any restrictions);
2) Group (refine one occupancy per selected group of atoms). Example:

ATOM      6  S   SO4     1       1.302   1.419   1.560  0.70
10.00           S
ATOM      7  O1  SO4     1       1.497   1.295   0.118  0.70
10.00           O
ATOM      8  O2  SO4     1       1.098   0.095   2.140  0.70
10.00           O
ATOM      9  O3  SO4     1       2.481   2.037   2.159  0.70
10.00           O
ATOM     10  O4  SO4     1       0.131   2.251   1.823  0.70
10.00           O

3) Constrained individual: refine occupancies of n atoms making sure
that the sum of occupancies over all n atoms is equal to 1.0.

What is not yet available (although almost done) is constrained group
occupancy refinement; this is similar to "3)":  refine one occupancy per
group of atoms making sure that the occupancies are equal to each other
within the group and the sum of the occupancies for an atom is 1.0. Example:

ATOM      6  S  ASO4     1       1.302   1.419   1.560  0.70
10.00           S
ATOM      7  O1 ASO4     1       1.497   1.295   0.118  0.70
10.00           O
ATOM      8  O2 ASO4     1       1.098   0.095   2.140  0.70
10.00           O
ATOM      9  O3 ASO4     1       2.481   2.037   2.159  0.70
10.00           O
ATOM     10  O4 ASO4     1       0.131   2.251   1.823  0.70
10.00           O
ATOM     11  S  BSO4     1       3.302   3.419   3.560  0.30
10.00           S
ATOM     12  O1 BSO4     1       3.497   3.295   2.118  0.30
10.00           O
ATOM     13  O2 BSO4     1       3.098   2.095   4.140  0.30
10.00           O
ATOM     14  O3 BSO4     1       4.481   4.037   4.159  0.30
10.00           O
ATOM     15  O4 BSO4     1       2.131   4.251   3.823  0.30
10.00           O

I'm working on this right now and hopefully it will be available soon.

Pavel.

Dr. Colin W. Levy wrote:
> Hi,
>
> What is the correct procedure in phenix for dealing with alternative
> conformations of side chains?
>
> Thanks
>
> Colin
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>

```

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