i have phenix 2007_08_18_1856, (and i think latest cci apps). i have a jumble of questions, i'll try step by step: [1 A] in phenix.autobuild, e.g. a SAD dataset, does the flag 'hires_file=w1.sca' (help says "Merge in hires data"), mean that phases will be extended to a high resolution limit as found in w1.sca? (vide infra) [1 B] can the labels be the same as the 'other' data (the documentation suggests this)? i have tried a few things like : phenix.autobuild data=resolve.mtz hires_file=high_resolution.mtz input_hires_labels='FPnat SIGFPnat' seq_file=seq.txt ... and i see Cell: [99.810997009277344, 99.810997009277344, 140.37300109863281, 90.0, 90.0, 90.0] New resolution: 2.20520367253 High-res file input labels: ['FPnat', 'SIGFPnat'] ... which is good, but the job promptly fails with this cryptic (to me) error message: ************************************************************ Failed to carry out AutoBuild_datafile_info_inputs: 'all_input_hires_labels' ************************************************************ ... (google:all_input_hires_labels and looking through docs quick didn't find it) -bryan
Hi Brian, The problem is in that version of phenix. I'm sorry about that! Can you possibly update to the current version...if that doesn't fix it then please let me know!
i have phenix 2007_08_18_1856, (and i think latest cci apps).
i have a jumble of questions, i'll try step by step:
[1 A] in phenix.autobuild, e.g. a SAD dataset, does the flag 'hires_file=w1.sca' (help says "Merge in hires data"), mean that phases will be extended to a high resolution limit as found in w1.sca? (vide infra)
Yes, that is correct.
[1 B] can the labels be the same as the 'other' data (the documentation suggests this)?
The labels are figured out and used totally independent of the other data (labels for hires are input_hires_labels as you mention below)
i have tried a few things like :
phenix.autobuild data=resolve.mtz hires_file=high_resolution.mtz input_hires_labels='FPnat SIGFPnat' seq_file=seq.txt
... and i see
Cell: [99.810997009277344, 99.810997009277344, 140.37300109863281, 90.0, 90.0, 90.0] New resolution: 2.20520367253 High-res file input labels: ['FPnat', 'SIGFPnat']
... which is good, but the job promptly fails with this cryptic (to me) error message:
************************************************************ Failed to carry out AutoBuild_datafile_info_inputs: 'all_input_hires_labels' ************************************************************
... (google:all_input_hires_labels and looking through docs quick didn't find it)
Yes, that's an error in autobuild, not your error. -Tom T
On Tue, 6 Nov 2007, Thomas C. Terwilliger wrote:
The problem is in that version of phenix. I'm sorry about that! Can you
that solved it, thanks.
[1 A] in phenix.autobuild, e.g. a SAD dataset, does the flag 'hires_file=w1.sca' (help says "Merge in hires data"), mean that phases will be extended to a high resolution limit as found in w1.sca? (vide infra)
Yes, that is correct.
ok, then i have to ask - is phenix merging each reflection? i.e, i wouldn't want to do this w/ a derivative and hi-res native, right?
[1 B] can the labels be the same as the 'other' data (the documentation suggests this)?
The labels are figured out and used totally independent of the other data (labels for hires are input_hires_labels as you mention below)
i have a job running OK, but it be nice to just confirm - when i specify input_labels='FreeR_flags', that will be the ONLY label taken - right? further - phenix will know to generate a new FreeR set only for hkl's of d_min beyond the ones i give it, i.e, keep the low-res FreeR, and add to it from among the high res data? -bryan
participants (2)
-
Bryan W. Lepore -
Thomas C. Terwilliger