From: Christian Roth
Date: 30 January 2012 13:54
Hi,
I want determine the spacegroup with pointless and it should directly write
out the mtz in the best sg. When I give a mtz with Structure Factor amplitude
pointless recognize the file (9 columns) change the space group and the new file
in the new space group has just 7 columns and FP and SigFP diappeared.
Running pointless with the option match to reference it works fine and the all
columns are there.
I tried it from commandline and Interface but it does not work. I use
pointless 1.6.5.
Has anyone a suggestion what goes wrong here. Does it prevent user error when
merged F's are given and omit them from the final mtz? However the input mtz
was in P1 so it should be not a problem.
Thanks in advance
Best Regards
Christian
----------
From: Phil Evans
Pointless can really only determine the space group from an unmerged file which wouldn't contain a merged amplitude F, so I'm not quite sure what you are trying to do
Can you send me the file & your command off-list & I'll check
best wishes
Phil
----------
From: Phil Evans
Dear Christian
When I run this data into Pointless it doesn't find any higher symmetry than I422. However, the data appear to be highly twinned so I would be wary of believing that.
If you put a merged file into Pointless, it can check for under-merging, but you can't really expect to use the output file as the program is now. It treats the file as if it was unmerged by squaring F to make a fake intensity, which is what is in the output file
You can take the raw output from XDS into Pointless, either XDS_ASCII.HKL or INTEGRATE.HKL, and that will give you a better idea of the symmetry - you can then scale the output file with Scala or Aimless if you wish, though I have no reason to suppose that it is better than CORRECT & XSCALE
I'm copying this to the BB for general informaiton
best wishes
Phil
On 30 Jan 2012, at 13:54, Christian Roth wrote:
Date: 30 January 2012 13:54
Hi,
I want determine the spacegroup with pointless and it should directly write
out the mtz in the best sg. When I give a mtz with Structure Factor amplitude
pointless recognize the file (9 columns) change the space group and the new file
in the new space group has just 7 columns and FP and SigFP diappeared.
Running pointless with the option match to reference it works fine and the all
columns are there.
I tried it from commandline and Interface but it does not work. I use
pointless 1.6.5.
Has anyone a suggestion what goes wrong here. Does it prevent user error when
merged F's are given and omit them from the final mtz? However the input mtz
was in P1 so it should be not a problem.
Thanks in advance
Best Regards
Christian
----------
From: Phil Evans
Pointless can really only determine the space group from an unmerged file which wouldn't contain a merged amplitude F, so I'm not quite sure what you are trying to do
Can you send me the file & your command off-list & I'll check
best wishes
Phil
----------
From: Phil Evans
Dear Christian
When I run this data into Pointless it doesn't find any higher symmetry than I422. However, the data appear to be highly twinned so I would be wary of believing that.
If you put a merged file into Pointless, it can check for under-merging, but you can't really expect to use the output file as the program is now. It treats the file as if it was unmerged by squaring F to make a fake intensity, which is what is in the output file
You can take the raw output from XDS into Pointless, either XDS_ASCII.HKL or INTEGRATE.HKL, and that will give you a better idea of the symmetry - you can then scale the output file with Scala or Aimless if you wish, though I have no reason to suppose that it is better than CORRECT & XSCALE
I'm copying this to the BB for general informaiton
best wishes
Phil
On 30 Jan 2012, at 13:54, Christian Roth wrote:
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