Content
2011-2013 User requests
2014-07-17 Jason Koglin, cxi...
Q:
Date: Thu, 17 Jul 2014 08:50:08 -0700 From: "Koglin, Jason" <koglin@slac.stanford.edu> To: "Dubrovin, Mikhail" <dubrovin@slac.stanford.edu> Cc: "Gaponenko, Igor" <gapon@slac.stanford.edu> Subject: RE: calib? The following have the geometry you just created for Ds2 and should also have the Ds1 geometry (2014-06-05 alignment of quads using lysozyme image from cxid2714 run 23). cxie1514 483 2014-07-13 2014-07-14 COHEN AINA PCS: Structural Studies of Multi-protein Complexes Involved in Transcriptional Initiation and Elongation cxie1414 482 2014-07-14 2014-07-14 Cascio, Duilio PCS: De Novo Phasing of Disease-Related Amyloidogenic Peptides using Iodine Derivatives cxie2614 480 2014-07-12 2014-07-13 HAU-RIEGE , STEFAN PCS: Progress toward single-molecule imaging with carbon nanotubes cxie2214 479 2014-07-13 2014-07-13 Feld, Geoffrey PCS: High-resolution X-ray diffraction from 2D membrane protein crystals of AQP0 cxie3014 478 2014-07-11 2014-07-12 Lawrence, Robert PCS: Comparative XFEL diffraction measurements on nanocrystals of human viruses cxie3214 477 2014-07-12 2014-07-12 Melcher, Karsten PCS: X-ray laser diffraction of AMP-activated kinase cxie4314 476 2014-07-10 2014-07-11 SIERRA, RAYMOND PCS: Liquid Injector Comparison for Protein Nanocrystallography cxie3914 475 2014-07-11 2014-07-11 ROBINSON, PHILIP PCS: Molecular mechanisms of transcription : the mediator. cxid6014 445 2014-06-26 2014-07-10 SCHLICHTING, ILME Ultra-fast events in Myoglobin Reaction Dynamics analyzed by Time-resolved Crystallography cxid5714 442 2014-06-25 2014-07-01 Schertler, Gebhard Femtosecond crystallography of G Protein-coupled Receptors cxic4414 440 2014-06-17 2014-06-25 CHEREZOV, VADIM Femtosecond Nanocrystallography of G Protein-Coupled Receptors in Lipidic Cubic Phase cxid9114 438 2014-06-10 2014-06-17 WAKATSUKI, SOICHI Use of Two-Color iSASE for SAD/MAD Phasing and Improved Intensity Measurements for ... cxid6214 436 2014-05-29 2014-06-10 Schmidt, Marius Dynamics in Biological Macromolecules with Femtosecond Time Resolution Same Ds2 Geometry but named Dsd and Ds1 geometry for 1-end from cxid6214/*/1-end.dat (i.e., 2014-06-05 alignment of quads using lysozyme image from cxid2714 run 23.) cxid2714 433 2014-05-16 2014-05-29 NEUTZE, RICHARD Ultrafast Time-resolved Wide Angle X-ray Scattering and ... By default we should make it so future experiments automatically inherit the previous experiment's latest calib data -- including all geometry and last pedestal -- as */0-end.dat The next experiment is: cxic8214 450 Hendricksonn, Wayne Single-wavelength Anomalous Diffraction (SAD) Phasing in Serial Femtosecond Crystallography (SFX) Jason
A: files from cxid9114 for ds1 and ds2 for
center, common_mode, marg_gap_shift, offset,offset_corr, tilt
were copied to
cxid6214, cxie1514, cxie1414, cxie2614, cxie2214, cxie3014, cxie3214, cxie4314, cxie3914, cxid6014, cxid5714, cxic4414, cxid2714(ds2 as dsd), cxic8214
2014-05-26 Marcin Sikorski, xcs84213-r0116
Q: How to switch following warning messages off?
"2014-05-27 16:05:04.203 [INF] {CSPadCalibPars} CSPadCalibPars.cpp:280 - In getCalibFileName(): the calibration file for the source=, type=center, run=115 is not found ... WARNING: Default CSPad alignment constants will be used."
A: Will need to change code...
2014-05-26 Thomas Kroll, cxib6414-r0023
Q1: how to save tiff images for cspad2x2
A1: See https://confluence.slac.stanford.edu/display/PCDS/Example+of+psana+analysis+for+CSPad2x2,
script: psana-cxib6714-r0023-cspad2x2.cfg
Q2: How to combine separate tiff images in a single file
A2: Use tiffcp command
2014-04-02 Silke Nelson, xppc7014
Q: in calibman the list of runs in the GUIDark is not updated for new xtc files
A:Request to RegDB did not update runs. Igor fixed this problem. Also add thread worker which checks for new xtc files, sends a signal and the list is updated automatically.
Problem fixed in
RegDB V00-01-26
CalibManager V00-00-28
Fix fill be available by default since ana-0.10.15
2014-03-13 Jason Koglin, cxii0114
Q: Could you please copy this over to cxii0114?
A: It is done, see CSPAD Alignment
2014-03-04 Jason Koglin, cxib6714 and cxi83714
Q: Could you please setup the DS1, DSD and SC1 140k, calib directory with appropriate files.
/reg/d/psdm/cxi/cxib6714/calib/
There is geometry data from cxi83714 that has been tagged in the elog 'Run Tables/Calibrations' page that you can use to do geometry
refinement.
A: 2014-03-05 CSPAD CxiDs1 alignment and new parameters deployed for cxib6714 and cxi83714.
2014-02-26 Andreas Schropp, MEC
Q: Need in example to process cspad-quad in mec
A: Example of psana analysis for CSPad2x2
2014-02-26 Jason Edwin Koglin, cxib3214
Q: need in dark calibration files for cxib3214 runs 1-302 marked as "dark".
A: produced and deployed using calibman:
ls /reg/d/psdm/CXI/cxib3214/calib/CsPad::CalibV1/CxiDs*.0:Cspad.0/*
2014-01-27 Cindy Bolme, mecb3114
Q: pedestal files and a psana config file to convert the CSpad data into corrected tiffs for mecb3114? This request is similar to what
you did for meca1113, but we used fewer cspads, so the config file might need to be altered slightly.
For the CSpad0 (quad) pedestal, r153 is the dark run that should be applied to runs 138-154. r323 is the dark run that should be applied to all other
runs 1-end.
For the CSpad2x2 pedestal, r8 is the dark run for runs 7-52. r64 is the dark run for all other runs 1-end.
We used several detectors during this experiment, so many of the runs do not have cspad data.
Thanks,
Cindy
A:
- Calibration files for dark runs were generated /reg/d/psdm/mec/mecb3114/calib/
for MecTargetChamber.0:Cspad.0
and MecTargetChamber.0:Cspad2x2.1 - r153 does not have MecTargetChamber.0:Cspad.0 data...
- Example of psana analysis for CSPad2x2
2014-01-24 Jason Edwin Koglin, CXI
Q: Mikhail, is it possible to setup ahead of time the calib files for all the PCS experiments being done at CXI this week (2
per night).
Experiment Id First Run Last Run Contact Description
cxic1114 404 Zhang, Xiaodong CXI screening proposal LC11
cxic1314 403 Volker Zickermann CXI screening proposal LC13
cxic1514 402 Ilme Schlichting CXI screening proposal LC15
cxic0314 401 Ilme Schlichting CXI screening proposal LC03
cxic1414 400 Zouni, Athina CXI screening proposal LC14, LB76
cxib9914 399 XU, Yibin CXI screening proposal LB99
cxic0914 398 Whisstock, James CXI screening proposal LC09
cxib9414 397 Richard Neutze CXI screening proposal LB94
A: copied from recent optical measurements for DS1 and DSD for center and tilt
2014-01-24 chun.hong.yoon cxib8914
Q: need in geometry correction files for /reg/d/psdm/CXI/cxib8914/calib
A: copied from recent optical measurements for DS1 and DSD for center and tilt
2014-01-17 Richard Sandberg, mecb3114
Q: We can see the Andor data with the script below, but we cannot convert it to tiff with the script we have currently. Could
you please help us with a script to pull that data down?
A: New module ImgAlgos::AndorImageProducer is added. See instructions of how to generate TIFF files in Andor image processing.
2014-01-15 Arianna Gleason, meca6013
Q: ImgAlgos::ImgSaveInFile stops psana job if image is missing in the event store.
A1 (Eric): remove missing source from cfg file
A2: ImgAlgos::ImgSaveInFile code is changed - warning message in stead of stop
A3: use pyimgalgos.image_save_in_file in stead of ImgAlgos::ImgSaveInFile
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