Re: [ccp4bb] Indexing question

[Andrew Leslie]

Dear Grace,

 There are two ways that you can do this. If you run 
POINTLESS/AIMLESS from iMosflm using the “Quickscale” option, you can tell 
POINTLESS to use the symmetry set at the indexing stage, using SETTINGS -> 
Processing options -> Sort Scale and Merge tab,, select the tick box “ Use 
iMosflm symmetry in Quickscale option”. So providing the C2 space group is 
selected at the indexing stage, it will keep that symmetry.

If running POINTLESS/AIMLESS through CCP4i, in the Data reduction - Pointless, 
Aimless, Ctruncate window, under the “Options for Pointless” box you can select 
an option:
Set primitive orthorhombic groups in cell length order (a On 18 Jul 2017, at 20:17, Grace Beggs  wrote:
> 
> Thank you, Andrew. How do I tell POINTLESS to keep C2?
> 
> Grace
> 
> 
> Grace Beggs
> Brennan lab
> Department of Biochemistry | Duke University
> Email: grace.be...@duke.edu 
> 
> 
> From: Andrew Leslie  >
> Sent: Tuesday, July 18, 2017 1:48:23 PM
> To: Grace Beggs; c...@ccp4.ac.uk  Laboratory
> Subject: Re: Indexing question
>  
> Dear Grace,
> 
>  POINTLESS will convert a C2 cell into I2 if this results a 
> beta angle closer to 90, so that the axes are closer to being orthogonal. All 
> CCP4 programs should work with I2, so this should not cause any issues. If 
> you want to keep the C@ space group, you can tell POINTLESS to keep C2 rather 
> than changing to I2.
> 
> Best wishes,
> 
> Andrew
> 
>> On 18 Jul 2017, at 18:42, Grace Beggs > > wrote:
>> 
>> To whom it may concern:
>> 
>> I am using version 7.2.1 of iMosflm. I have indexed, refined and 
>> successfully integrated and scaled my data with the space group C 1 2 1. 
>> Although the log file output after running aimless states the space group as 
>> C 1 2 1, when I load the mtz file into Phenix it states the space group is I 
>> 1 2 1. Could imosflm be writing the mtz file as I 1 2 1? How does one 
>> correct this? I 1 2 1 is not a standard space group.
>> 
>> Thank you,
>> Grace Beggs
>> 
>> 
>> Grace Beggs
>> Brennan lab
>> Department of Biochemistry | Duke University
>> Email: grace.be...@duke.edu 

[ccp4bb] indexing(?) question in P21

[wtempel]

Hello all,
I am puzzled by this situation:
I have two different crystal of the same protein, in the presence, one in
the absence of a ligand.
Both structures refine nicely in space group P21.
Cell constants (a,b,c,beta) are (i) 61,124,61,119 (ac by a hair) and (ii)
 59,125,61,118. There is a SINGLE protein molecule in the ASU. To
facilitate future analysis and comparison between both structures, I have
tried (incl. reindexing) to refine both structures with as similar as
possible translational/rotational states as possible. A failed to do any
better than having them offset by approx. 32A exactly along the a-xis.
Considering the pseudo-hexagonal cell and the extent of the offset being so
close to a/2, c/2 or b/3, I have the feeling that I am missing something.
What could it be?
Thank you as always.
Wolfram Tempel

Re: [ccp4bb] indexing(?) question in P21

[Phil Jeffrey]

Wolfram,

Did you solve these structures independently by molecular replacement ? 
 It sounds like your two solutions might be related by alternative 
origins (0,1/2 along a,c).  If you translate the second example along 
the a axis by -a/2 does it refine with similar R-factors ?


Phil Jeffrey
Princeton

On 4/19/12 1:35 PM, wtempel wrote:

Hello all,
I am puzzled by this situation:
I have two different crystal of the same protein, in the presence, one
in the absence of a ligand.
Both structures refine nicely in space group P21.
Cell constants (a,b,c,beta) are (i) 61,124,61,119 (ac by a hair) and
(ii) 59,125,61,118. There is a SINGLE protein molecule in the ASU. To
facilitate future analysis and comparison between both structures, I
have tried (incl. reindexing) to refine both structures with as similar
as possible translational/rotational states as possible. A failed to do
any better than having them offset by approx. 32A exactly along the
a-xis. Considering the pseudo-hexagonal cell and the extent of the
offset being so close to a/2, c/2 or b/3, I have the feeling that I am
missing something. What could it be?
Thank you as always.
Wolfram Tempel

Re: [ccp4bb] indexing(?) question in P21 - solved

[Bryan Lepore]

On Thu, Apr 19, 2012 at 4:28 PM, wtempel wtem...@gmail.com wrote:
 I went ahead and explicitly applied that +0.5*a translation. [...] It turns 
 out that after the origin
 shift, some distances between equivalent atoms of the two structures
 exceeded 3A

I'd be interested to know if cphasematch would reach the exact same
solution - i.e. how did you know to shift along a?

  A (sic) failed to do any better than having them offset by approx. 32A 
 exactly along the a-xis.

isn't this the same thing that was done above?

-Bryan