RE: [phenixbb] conversion from h3 to r3 with phenix apps 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: [email protected] 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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