# [phenixbb] conversion from h3 to r3 with phenix apps

Green, Todd green at cbse.uab.edu
Fri Aug 10 15:01:58 PDT 2007

```I'm actually not sure that it's not orthorhombic. I know looking at the cell lengths and angles makes it very inviting to the cubic cell and i have been working with that as a possibility. i do have a real good suspicion that I have a pseudo-cubic cell. I can do molecular replacement in the cubic space group but am missing some density that I think should be there. I wanted to do molecular replacement in the rhombohedral setting and ultimately the lower symmetry space group too and see if I pick that density up. This is why I wanted to know how to convert the h3 to r3 setting. the h3 cell is a nightmare for my computer!

as a side note not all of the crystals, process in the primitive lattice, but all process as rhombohedral. That probably means that I have a two different types of crystals more than anything else, etc etc etc. cross-xtal averaging is another reason to i wanted to figure out the setting difference.

I have previously run one of my datasets processed in p1 thru Xtriage, it said:

Exploring higher metric symmetry

The point group of data as dictated by the space group is P 1
the point group in the niggli setting is P 1
The point group of the lattice is P 4 3 2
A summary of R values for various possible point groups follow.

------------------------------------------------------------------------------------------------
| Point group               | mean R_used | max R_used | mean R_unused | min R_unused | choice |
------------------------------------------------------------------------------------------------
| P 1                       | None        | None       | 0.362         | 0.103        | <---   |
| P 2 3                     | 0.134       | 0.169      | 0.478         | 0.478        |        |
| P 4                       | 0.152       | 0.488      | 0.377         | 0.164        |        |
| C 1 2 1 (z,x+y,-x+y)      | 0.489       | 0.489      | 0.337         | 0.103        |        |
| P 4 2 2 (c,a,b)           | 0.266       | 0.481      | 0.481         | 0.478        |        |
| P 1 1 2                   | 0.110       | 0.110      | 0.221         | 0.103        |        |
| P 2 1 1                   | 0.107       | 0.107      | 0.290         | 0.110        |        |
| R 3 2 :R                  | 0.481       | 0.483      | 0.109         | 0.103        |        |
| C 1 2 1 (x+y,-x+y,z)      | 0.492       | 0.492      | 0.269         | 0.103        |        |
| P 2 2 2                   | 0.109       | 0.110      | 0.481         | 0.478        |        |
| C 2 2 2 (x-y,x+y,z)       | 0.190       | 0.478      | 0.339         | 0.103        |        |
| P 4 (c,a,b)               | 0.454       | 0.476      | 0.272         | 0.110        |        |
| C 1 2 1 (x+y,z,x-y)       | 0.483       | 0.483      | 0.351         | 0.103        |        |
| C 1 2 1 (-x+y,z,x+y)      | 0.486       | 0.486      | 0.351         | 0.103        |        |
| P 1 2 1                   | 0.103       | 0.103      | 0.343         | 0.110        |        |
| R 3 2 :h (x+z,y-z,-x+y+z) | 0.488       | 0.492      | 0.109         | 0.103        |        |
| P 4 2 2 (b,c,a)           | 0.181       | 0.486      | 0.480         | 0.478        |        |
| R 3 :h (x+z,y-z,-x+y+z)   | 0.148       | 0.148      | 0.256         | 0.103        |        |
| C 2 2 2 (z,x-y,x+y)       | 0.426       | 0.489      | 0.309         | 0.110        |        |
| R 3 2 :h (-x+y+z,x+z,y-z) | 0.484       | 0.489      | 0.109         | 0.103        |        |
| C 2 2 2 (-x+y,z,x+y)      | 0.386       | 0.486      | 0.327         | 0.110        |        |
| P 4 2 2                   | 0.243       | 0.492      | 0.386         | 0.169        |        |
| R 3 :h (-x+y+z,x+z,y-z)   | 0.153       | 0.153      | 0.256         | 0.103        |        |
| R 3 :h (y-z,-x+y+z,x+z)   | 0.164       | 0.164      | 0.256         | 0.103        |        |
| P 4 3 2                   | 0.362       | 0.492      | None          | None         |        |
| C 1 2 1 (x-y,x+y,z)       | 0.478       | 0.478      | 0.269         | 0.103        |        |
| R 3 2 :h (y-z,-x+y+z,x+z) | 0.486       | 0.492      | 0.109         | 0.103        |        |
| R 3 :R                    | 0.169       | 0.169      | 0.256         | 0.103        |        |
| P 4 (b,c,a)               | 0.419       | 0.475      | 0.290         | 0.110        |        |
| C 1 2 1 (z,x-y,x+y)       | 0.481       | 0.481      | 0.337         | 0.103        |        |
------------------------------------------------------------------------------------------------

R_used: mean and maximum R value for symmetry operators *used* in this point group
R_unused: mean and minimum R value for symmetry operators *not used* in this point group
The likely point group of the data is:  P 1

Possible space groups in this point groups are:
Unit cell: (375.144, 375.711, 377.723, 90.002, 90.034, 90.094)
Space group: P 1 (No. 1)

what does this say to you?

Thanks in advance-
Todd

-----Original Message-----
From: phenixbb-bounces at phenix-online.org on behalf of Peter Zwart
Sent: Fri 8/10/2007 4:35 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] conversion from h3 to r3 with phenix apps

Hi Todd,

Are you sure this is not cubic? You could run xtriage and find out
relatively easely.

I suggest you give phenix.xmanip a try for reindexing or try to use the
following one-liner:

iotbx.reflection_file_converter data.sca
--change-of-basis=to_niggli_cell --sca=niggli.sca

Cheers

Peter

Green, Todd wrote:
>
> Hello all,
>
> I have what i believe to be a rhombohedral crystal that has an
> insanely large cell with the hexagonal setting:
>
> 533.026   533.026   652.887    90.000    90.000   120.000
>
> and a modestly large cell comparatively with the rhombohedral setting:
>
> 377 377 377 90 90 90
>
> I should be able to easily reindex to the smaller cell in scalepack
> but for some reason i'm not getting it to work correctly. Rather than
> struggle further on a friday afternoon, i figured that i'd give a
> phenix app a try. i assume xtriage can do this, can someone point me
> in the correct direction?
>
> thanks in advance-
> Todd
>
> ------------------------------------------------------------------------
>
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