What does mmtbx.twin_map_utils output?
Specifically I'm asking about the obs_and_calc.mtz file it produces. Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
obs : obs data calc: Fatoms+Fbulk No twinning involved in computation of calc For some reason, the R value between Fcalc for twin related reflections are all about 14%. I guess you have pseudo symmetry somehow, but I still would not exclude P422 ... Francis E Reyes wrote:
Specifically I'm asking about the obs_and_calc.mtz file it produces.
Thanks
FR
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
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The model was rebuilt using P422, but I couldn't get the R/Rfree's down from the mid 30s, despite the entire model being built. Thinking I had a twin problem, I scaled it to C2, the lowest symmetry space group the data collection would allow. I was enthused,however, that twin_map_utils did show a round of refinement where R/Rfree was 30/30 at 2.6A, though I/Sig should be > 2 at 2.8 A. I was hopefully trying to get a model to refine using the way twin_map_utils did to produce the low r/rfree until I hit the phenix.refine twinning bug.. FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D On Sep 11, 2007, at 12:32 PM, Peter Zwart wrote:
obs : obs data calc: Fatoms+Fbulk
No twinning involved in computation of calc
For some reason, the R value between Fcalc for twin related reflections are all about 14%. I guess you have pseudo symmetry somehow, but I still would not exclude P422 ...
Francis E Reyes wrote:
Specifically I'm asking about the obs_and_calc.mtz file it produces.
Thanks
FR
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
--------------------------------------------------------------------- ---
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I am refining it myself now, and I think that the problem you describe has been solved locally. The twin map utils unfortunatly doesn't pick jup the free set automatically, which probably is the reason why the free R = the R, unless you specify the free set in from the command line. Including twinning in refinement will almost always get your R value to something lower than when not including twinning; even if the data is not twinned ... Did you try using a TLS model in the P422 case? Furthermore, is the data P422, or is there evidence for the sg to be P4x2y2? Thanks Peter Francis E Reyes wrote:
The model was rebuilt using P422, but I couldn't get the R/Rfree's down from the mid 30s, despite the entire model being built. Thinking I had a twin problem, I scaled it to C2, the lowest symmetry space group the data collection would allow. I was enthused,however, that twin_map_utils did show a round of refinement where R/Rfree was 30/30 at 2.6A, though I/Sig should be > 2 at 2.8 A. I was hopefully trying to get a model to refine using the way twin_map_utils did to produce the low r/rfree until I hit the phenix.refine twinning bug..
FR
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
On Sep 11, 2007, at 12:32 PM, Peter Zwart wrote:
obs : obs data calc: Fatoms+Fbulk
No twinning involved in computation of calc
For some reason, the R value between Fcalc for twin related reflections are all about 14%. I guess you have pseudo symmetry somehow, but I still would not exclude P422 ...
Francis E Reyes wrote:
Specifically I'm asking about the obs_and_calc.mtz file it produces.
Thanks
FR
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
------------------------------------------------------------------------
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participants (2)
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Francis E Reyes -
Peter Zwart