[phenixbb] conversion from h3 to r3 with phenix apps
Peter Zwart
PHZwart at lbl.gov
Fri Aug 10 15:24:53 PDT 2007
Hi Todd,
This table tells me that the data in P1 doesn't merge very well and that
limits for what is reasonable are maybe set to tight for your case.
Try using the keyword tanh_location=0.11 and see what happens.
Just looking at the table though, there seem to be a number of options
to be considered:
P1: one unused symmetry operator present with R value equal 10%. Not a
good sign, sg is too low
P432: ONe operator has an R value of 47%. Not a good sign, sg is too high
A couple of flavours of R3.
| R 3 :h (x+z,y-z,-x+y+z) | 0.148 | 0.148 | 0.256 |
0.103 |
| 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 |
| R 3 :R | 0.169 | 0.169 |
0.256 | 0.103 |
From the last column it is clearly seen that an operator is present
with a R-value equal to 10%, but is not used in the point group. The
point group might be too low.
The flavours of R32 don't work, as a operator is used that has a high R
value:
| R 3 2 :h (-x+y+z,x+z,y-z) | 0.484 | 0.489 | 0.109 |
0.103
| R 3 2 :h (y-z,-x+y+z,x+z) | 0.486 | 0.492 | 0.109 |
0.103
These options are nice(ish):
| P 2 3 | 0.134 | 0.169 |
0.478 | 0.478 | |
| P 2 2 2 | 0.109 | 0.110 |
0.481 | 0.478 | |
| P 4 2 2 (b,c,a) | 0.181 | 0.486 |
0.480 | 0.478 | |
Do you have any indication that your data is twinned?
Peter
Green, Todd wrote:
>
> 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
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
> >
>
>
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