Thanks a lot for taking time out to make these videos. Its very useful. It would be great if you could make a series/playlist where you go from synchrotron image files to pdb using Phenix. That would give novice users like me a very good understanding of the program and how to solve a xtal structure from start to finish. Once again thanks for your help.
Thanks for your feedback! Such a series or playlist would be certainly helpful but I fear it goes beyond the scope of this tutorial channel about Phenix programs. If you want to learn more about a specific tool, let us know!
I'm a beginner. Could you please comment on these. (1) While refining, I found these options in Data labels: I-obs, SIGI-obs ; F-obs-filtered; SIGF-obs-filtered. How to choose the best one? Is there any rule for this? Thanks for help. (2) I am using Phenix.refine default parameters. How do I know all are ok for my structures (Resol: ~1.8A). I did not find any problem in molprobity or validation report. That means all are ok. Right?
(1) I-obs and SIGI-obs are the experimental data. The F-obs-filtered array comes from conversion from intensities to structure factors, including some outlier filtering. I suggest choosing I-obs and SIGI-obs for input. (2) At 1.8 Å, default parameters should be OK, but it always depends on the individual case, f.ex. if you have NCS, you might want to try NCS restraints (and if you don't, no need to apply them); if there are no problems in validation reports and if you don't see obvious issues in the maps (check in a molecular viewer, such as Coot), then your strategy is most likely fine.
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Thanks a lot for taking time out to make these videos. Its very useful. It would be great if you could make a series/playlist where you go from synchrotron image files to pdb using Phenix. That would give novice users like me a very good understanding of the program and how to solve a xtal structure from start to finish. Once again thanks for your help.
Thanks for your feedback!
Such a series or playlist would be certainly helpful but I fear it goes beyond the scope of this tutorial channel about Phenix programs.
If you want to learn more about a specific tool, let us know!
I'm a beginner. Could you please comment on these. (1) While refining, I found these options in Data labels: I-obs, SIGI-obs ; F-obs-filtered; SIGF-obs-filtered. How to choose the best one? Is there any rule for this? Thanks for help. (2) I am using Phenix.refine default parameters. How do I know all are ok for my structures (Resol: ~1.8A). I did not find any problem in molprobity or validation report. That means all are ok. Right?
(1) I-obs and SIGI-obs are the experimental data. The F-obs-filtered array comes from conversion from intensities to structure factors, including some outlier filtering. I suggest choosing I-obs and SIGI-obs for input.
(2) At 1.8 Å, default parameters should be OK, but it always depends on the individual case, f.ex. if you have NCS, you might want to try NCS restraints (and if you don't, no need to apply them); if there are no problems in validation reports and if you don't see obvious issues in the maps (check in a molecular viewer, such as Coot), then your strategy is most likely fine.
Need a paired-refinement tutorial!
:P
i have my own pdb structure. how can I get my reflection file??
For refinement, you would get a reflection file from a diffraction experiment.