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Can you attach the pointless log file for a job run WITHOUT requesting any space group. Pointless will consider all possible space groups which satisfy the bravais lattice and symmetry considerations. In general it will preferred to work in P symmetry if possible but i could comment better if you sent that log.

Eleanor

On 24 January 2016 at 21:53, Gyl <[log in to unmask]> wrote:
Thank you for the clarification, James. I think I found the right option in Aimless.

On Sun, Jan 24, 2016 at 10:45 PM, James Holton <[log in to unmask]> wrote:
I expect your space group is getting changed by a program called POINTLESS, which is generally the entry point for XDS data into a format that AIMLESS can read.  Documentation is here:
http://www.ccp4.ac.uk/html/pointless.html

  I'm not sure what interface you are using, but if you can find a way to get the string "CHOOSE SPACEGROUP P3121" (where "P3121" is your space group of choice) into the input of POINTLESS, then I think that will do what you want.

Of course, as long as your scaling is done in the point group of the space group you want, it might be easier to just change the space group after scaling with REINDEX.

Remember:
There are 14 Bravais lattices, and this decision must be made before integrating the spots
There are 12 point groups (for chiral stuff), and this decision must be made before scaling and merging
There are 65 space groups (for chiral stuff), and this decision must be made before phasing

There are, of course, a long list of clever ways around these rules, but in general if you want to change point group, then you will probably want to do scaling again.  If you want to change Bravais lattice then you probably want to go back to integration (need diffraction images).  But, if you are in the right point group and all you want to do is change to another space group within that point group, then you can just change the file header.  Unless, of course, you have phases (and a pdb file counts), then you generally want to "re-do" whatever you did to get those phases in the new space group (MR, MAD, SAD, MIR, etc.).

That said, if "the programs" are changing your space group from the one you want, then 9 times out of 10 they are right and you are wrong.  Make sure you look at the log files and documentation long enough to understand why the automated decision is being made.  Its okay to disagree, but only after you have checked.

-James Holton
MAD Scientist


On 1/24/2016 11:31 AM, Gyl wrote:
Dear All,

Pardon the newbie question. I processed my data in XDS and scaled in Aimless. How can I stop Aimless from changing the space group I picked in XDS? Thank you in advance.

Sincerely,
Gyl